WorldWideScience

Sample records for structure alignment ontology

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

    Science.gov (United States)

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

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

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

    OpenAIRE

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

    2014-01-01

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

  5. Use artificial neural network to align biological ontologies.

    Science.gov (United States)

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

    2008-09-16

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

  6. 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.

  7. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    National Research Council Canada - National Science Library

    Starz, James; Roberts, Joe

    2008-01-01

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

  10. Experiences from the anatomy track in the ontology alignment evaluation initiative.

    Science.gov (United States)

    Dragisic, Zlatan; Ivanova, Valentina; Li, Huanyu; Lambrix, Patrick

    2017-12-04

    One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to align the Foundational Model of Anatomy and the OpenGalen Anatomy Model. Since 2007 the ontologies used in the track are the Adult Mouse Anatomy and a part of the NCI Thesaurus. Since 2015 the data in the Anatomy track is also used in the Interactive track of the Ontology Alignment Evaluation Initiative. In this paper we focus on the Anatomy track in the years 2007-2016 and the Anatomy part of the Interactive track in 2015-2016. We describe the data set and the changes it went through during the years as well as the challenges it poses for ontology alignment systems. Further, we give an overview of all systems that participated in the track and the techniques they have used. We discuss the performance results of the systems and summarize the general trends. About 50 systems have participated in the Anatomy track. Many different techniques were used. The most popular matching techniques are string-based strategies and structure-based techniques. Many systems also use auxiliary information. The quality of the alignment has increased for the best performing systems since the beginning of the track and more and more systems check the coherence of the proposed alignment and implement a repair strategy. Further, interacting with an oracle is beneficial.

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

    Science.gov (United States)

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

    2017-12-02

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

  12. 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.

  13. 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.

  14. Using C-OWL for the Alignment and Merging of Medical Ontologies

    NARCIS (Netherlands)

    Stuckenschmidt, Heiner; van Harmelen, Frank; Serafini, Luciano; Bouquet, Paolo; Giunchiglia, Fausto

    2004-01-01

    A number of sophisticated medical ontologies have been created over the past years. With their de-velopment the need for supporting the alignment of different ontologies is gaining importance. We proposed C-OWL, an extension of the Web Ontology Language OWL that supports alignment mappings between

  15. [Towards a structuring fibrillar ontology].

    Science.gov (United States)

    Guimberteau, J-C

    2012-10-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

    Oliveira, Daniela; Pesquita, Catia

    2018-01-09

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

  18. 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

  19. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

    2018-01-01

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

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

    Science.gov (United States)

    Cox, S. J. D.

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  2. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

  3. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  4. 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...

  5. Using ontology network structure in text mining.

    Science.gov (United States)

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

    2010-11-13

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

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

    Science.gov (United States)

    Glick, David

    2016-10-01

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

  7. A new paradigm for continuous alignment of business and IT: combining enterprise architecture modeling and enterprise ontology

    CSIR Research Space (South Africa)

    Hinkelmann, K

    2015-08-01

    Full Text Available Alignment of Business and IT: Combining Enterprise Architecture Modeling and Enterprise Ontology Knut Hinkelmann, School of Business, FHNW University of Applied Sciences and Arts Northwestern Switzerland, 4600 Olten, Switzerland and Department... initiatives, the architecture at the start of a development might not be appropriate anymore when the new business processes and information systems are rolled out. The grand challenge for today's enterprises, which we deal with in this research...

  8. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is re......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious...

  9. 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

  10. The Relationship between User Expertise and Structural Ontology Characteristics

    Science.gov (United States)

    Waldstein, Ilya Michael

    2014-01-01

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

  11. NegGOA: negative GO annotations selection using ontology structure.

    Science.gov (United States)

    Fu, Guangyuan; Wang, Jun; Yang, Bo; Yu, Guoxian

    2016-10-01

    Predicting the biological functions of proteins is one of the key challenges in the post-genomic era. Computational models have demonstrated the utility of applying machine learning methods to predict protein function. Most prediction methods explicitly require a set of negative examples-proteins that are known not carrying out a particular function. However, Gene Ontology (GO) almost always only provides the knowledge that proteins carry out a particular function, and functional annotations of proteins are incomplete. GO structurally organizes more than tens of thousands GO terms and a protein is annotated with several (or dozens) of these terms. For these reasons, the negative examples of a protein can greatly help distinguishing true positive examples of the protein from such a large candidate GO space. In this paper, we present a novel approach (called NegGOA) to select negative examples. Specifically, NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein to choose negative examples of the protein. We compare NegGOA with other negative examples selection algorithms and find that NegGOA produces much fewer false negatives than them. We incorporate the selected negative examples into an efficient function prediction model to predict the functions of proteins in Yeast, Human, Mouse and Fly. NegGOA also demonstrates improved accuracy than these comparing algorithms across various evaluation metrics. In addition, NegGOA is less suffered from incomplete annotations of proteins than these comparing methods. The Matlab and R codes are available at https://sites.google.com/site/guoxian85/neggoa gxyu@swu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

    Science.gov (United States)

    Zheng, Ling; Chen, Yan; Elhanan, Gai; Perl, Yehoshua; Geller, James; Ochs, Christopher

    2018-05-28

    In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often become fertile ground for quality assurance (QA) in ontologies. They should be audited first. One example of complex concepts is given by "overlapping concepts" (to be defined below.) Historically, a different auditing methodology had to be developed for every single ontology. For better scalability and efficiency, it is desirable to identify family-wide QA methodologies. Each such methodology would be applicable to a whole family of similar ontologies. In past research, we had divided the 685 ontologies of BioPortal into families of structurally similar ontologies. We showed for four ontologies of the same large family in BioPortal that "overlapping concepts" are indeed statistically significantly more likely to exhibit errors. In order to make an authoritative statement concerning the success of "overlapping concepts" as a methodology for a whole family of similar ontologies (or of large subhierarchies of ontologies), it is necessary to show that "overlapping concepts" have a higher likelihood of errors for six out of six ontologies of the family. In this paper, we are demonstrating for two more ontologies that "overlapping concepts" can successfully predict groups of concepts with a higher error rate than concepts from a control group. The fifth ontology is the Neoplasm subhierarchy of the National Cancer Institute thesaurus (NCIt). The sixth ontology is the Infectious Disease subhierarchy of SNOMED CT. We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts." First, an erroneous "overlapping concept" can help with discovering other erroneous "non-overlapping concepts" in its vicinity

  13. ROMIE, une approche d'alignement d'ontologies à base d'instances

    OpenAIRE

    Elbyed , Abdeltif

    2009-01-01

    System interoperability is an important issue, widely recognized in information technology intensive organizations and in the research community of information systems. The wide adoption of the World Wide Web to access and distribute information further stresses the need for system interoperability. Initiative solutions like the Semantic Web facilitate the localization and the integration of the data in a more intelligent way via the use of ontologies. The Semantic Web offers a compelling vis...

  14. Alignment of the MSGC barrel support structure

    International Nuclear Information System (INIS)

    Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala; Antti, Onnela

    1999-01-01

    The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

  15. Alignment of the MSGC barrel support structure

    Energy Technology Data Exchange (ETDEWEB)

    Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala [HIP, Helsinki Institute of Physics, CERN/EP, Geneva (Switzerland); Antti, Onnela [CERN, Conseil Europeen pour la recherche nucleaire, Laboratoire europeen pour la physique des particules, Geneve (Switzerland)

    1999-07-01

    The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

  16. An ontology-driven tool for structured data acquisition using Web forms.

    Science.gov (United States)

    Gonçalves, Rafael S; Tu, Samson W; Nyulas, Csongor I; Tierney, Michael J; Musen, Mark A

    2017-08-01

    Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web. We tackle the problem of generating Web-based assessment forms from OWL ontologies, and aggregating input gathered through these forms as an ontology of "semantically-enriched" form data that can be queried using an RDF query language, such as SPARQL. We developed an ontology-based structured data acquisition system, which we present through its specific application to the clinical functional assessment domain. We found that data gathered through our system is highly amenable to automatic analysis using queries. We demonstrated how ontologies can be used to help structuring Web-based forms and to semantically enrich the data elements of the acquired structured data. The ontologies associated with the enriched data elements enable automated inferences and provide a rich vocabulary for performing queries.

  17. Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

    Science.gov (United States)

    Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

    2010-05-24

    We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

  18. Aligning ontologies and integrating textual evidence for pathway analysis of microarray data

    Energy Technology Data Exchange (ETDEWEB)

    Gopalan, Banu; Posse, Christian; Sanfilippo, Antonio P.; Stenzel-Poore, Mary; Stevens, S.L.; Castano, Jose; Beagley, Nathaniel; Riensche, Roderick M.; Baddeley, Bob; Simon, R.P.; Pustejovsky, James

    2006-10-08

    Expression arrays are introducing a paradigmatic change in biology by shifting experimental approaches from single gene studies to genome-level analysis, monitoring the ex-pression levels of several thousands of genes in parallel. The massive amounts of data obtained from the microarray data needs to be integrated and interpreted to infer biological meaning within the context of information-rich pathways. In this paper, we present a methodology that integrates textual information with annotations from cross-referenced ontolo-gies to map genes to pathways in a semi-automated way. We illustrate this approach and compare it favorably to other tools by analyzing the gene expression changes underlying the biological phenomena related to stroke. Stroke is the third leading cause of death and a major disabler in the United States. Through years of study, researchers have amassed a significant knowledge base about stroke, and this knowledge, coupled with new technologies, is providing a wealth of new scientific opportunities. The potential for neu-roprotective stroke therapy is enormous. However, the roles of neurogenesis, angiogenesis, and other proliferative re-sponses in the recovery process following ischemia and the molecular mechanisms that lead to these processes still need to be uncovered. Improved annotation of genomic and pro-teomic data, including annotation of pathways in which genes and proteins are involved, is required to facilitate their interpretation and clinical application. While our approach is not aimed at replacing existing curated pathway databases, it reveals multiple hidden relationships that are not evident with the way these databases analyze functional groupings of genes from the Gene Ontology.

  19. THE PRINCIPLES AND METHODS OF INFORMATION AND EDUCATIONAL SPACE SEMANTIC STRUCTURING BASED ON ONTOLOGIC APPROACH REALIZATION

    Directory of Open Access Journals (Sweden)

    Yurij F. Telnov

    2014-01-01

    Full Text Available This article reveals principles of semantic structuring of information and educational space of objects of knowledge and scientific and educational services with use of methods of ontologic engineering. Novelty of offered approach is interface of ontology of a content and ontology of scientific and educational services that allows to carry out effective composition of services and objects of knowledge according to models of professional competences and requirements being trained. As a result of application of methods of information and educational space semantic structuring integration of use of the diverse distributed scientific and educational content by educational institutions for carrying out scientific researches, methodical development and training is provided.

  20. Anatomy Ontology Matching Using Markov Logic Networks

    Directory of Open Access Journals (Sweden)

    Chunhua Li

    2016-01-01

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

  1. Ontology Matching with Semantic Verification.

    Science.gov (United States)

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

    2009-09-01

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

  2. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  3. QUASAR--scoring and ranking of sequence-structure alignments.

    Science.gov (United States)

    Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

    2005-12-15

    Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

  4. Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

    Science.gov (United States)

    Nigam, Rajni; Munzenmaier, Diane H; Worthey, Elizabeth A; Dwinell, Melinda R; Shimoyama, Mary; Jacob, Howard J

    2013-11-22

    The Rat Genome Database (RGD) ( http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed. The Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######). As rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This

  5. Fine-tuning structural RNA alignments in the twilight zone

    Directory of Open Access Journals (Sweden)

    Schirmer Stefanie

    2010-04-01

    Full Text Available Abstract Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

  6. Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

    Science.gov (United States)

    Bibault, Jean-Emmanuel; Zapletal, Eric; Rance, Bastien; Giraud, Philippe; Burgun, Anita

    2018-01-01

    Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our "record-and-verify" system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique-Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).

  7. Alignment between Protostellar Outflows and Filamentary Structure

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Lee, Katherine I.; Goodman, Alyssa A. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA (United States); Vorobyov, Eduard I. [Institute of Fluid Mechanics and Heat Transfer, TU Wien, Vienna, A-1060 (Austria); Tobin, John J. [Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, 440 W. Brooks Street, Norman, OK 73019 (United States); Pineda, Jaime E. [Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse 1, 85748 Garching (Germany); Offner, Stella S. R. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Kristensen, Lars E. [Centre for Star and Planet Formation, Niels Bohr Institute and Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K (Denmark); Jørgensen, Jes K. [Niels Bohr Institute and Center for Star and Planet Formation, Copenhagen University, DK-1350 Copenhagen K. (Denmark); Bourke, Tyler L. [SKA Organization, Jodrell Bank Observatory, Lower Withington, Macclesfield, Cheshire SK11 9DL (United Kingdom); Arce, Héctor G. [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Plunkett, Adele L., E-mail: ian.stephens@cfa.harvard.edu [European Southern Observatory, Av. Alonso de Cordova 3107, Vitacura, Santiago de Chile (Chile)

    2017-09-01

    We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

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

    Directory of Open Access Journals (Sweden)

    Górny Z.

    2014-03-01

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

  9. Ontological Planning

    Directory of Open Access Journals (Sweden)

    Ahmet Alkan

    2017-12-01

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

  10. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  11. From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.

    Science.gov (United States)

    Elhanan, Gai; Ochs, Christopher; Mejino, Jose L V; Liu, Hao; Mungall, Christopher J; Perl, Yehoshua

    2017-06-01

    To examine whether disjoint partial-area taxonomy, a semantically-based evaluation methodology that has been successfully tested in SNOMED CT, will perform with similar effectiveness on Uberon, an anatomical ontology that belongs to a structurally similar family of ontologies as SNOMED CT. A disjoint partial-area taxonomy was generated for Uberon. One hundred randomly selected test concepts that overlap between partial-areas were matched to a same size control sample of non-overlapping concepts. The samples were blindly inspected for non-critical issues and presumptive errors first by a general domain expert whose results were then confirmed or rejected by a highly experienced anatomical ontology domain expert. Reported issues were subsequently reviewed by Uberon's curators. Overlapping concepts in Uberon's disjoint partial-area taxonomy exhibited a significantly higher rate of all issues. Clear-cut presumptive errors trended similarly but did not reach statistical significance. A sub-analysis of overlapping concepts with three or more relationship types indicated a much higher rate of issues. Overlapping concepts from Uberon's disjoint abstraction network are quite likely (up to 28.9%) to exhibit issues. The results suggest that the methodology can transfer well between same family ontologies. Although Uberon exhibited relatively few overlapping concepts, the methodology can be combined with other semantic indicators to expand the process to other concepts within the ontology that will generate high yields of discovered issues. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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 tr...

  13. An Application of Structural Equation Modeling for Developing Good Teaching Characteristics Ontology

    Science.gov (United States)

    Phiakoksong, Somjin; Niwattanakul, Suphakit; Angskun, Thara

    2013-01-01

    Ontology is a knowledge representation technique which aims to make knowledge explicit by defining the core concepts and their relationships. The Structural Equation Modeling (SEM) is a statistical technique which aims to explore the core factors from empirical data and estimates the relationship between these factors. This article presents an…

  14. Alignment structures in ferroelectric liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Islam, N.U

    1998-07-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S{sub C} phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes

  15. Alignment structures in ferroelectric liquid crystals

    International Nuclear Information System (INIS)

    Islam, N.U.

    1998-01-01

    Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S C phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes an

  16. Facet Theory and the Mapping Sentence As Hermeneutically Consistent Structured Meta-Ontology and Structured Meta-Mereology

    Science.gov (United States)

    Hackett, Paul M. W.

    2016-01-01

    When behavior is interpreted in a reliable manner (i.e., robustly across different situations and times) its explained meaning may be seen to possess hermeneutic consistency. In this essay I present an evaluation of the hermeneutic consistency that I propose may be present when the research tool known as the mapping sentence is used to create generic structural ontologies. I also claim that theoretical and empirical validity is a likely result of employing the mapping sentence in research design and interpretation. These claims are non-contentious within the realm of quantitative psychological and behavioral research. However, I extend the scope of both facet theory based research and claims for its structural utility, reliability and validity to philosophical and qualitative investigations. I assert that the hermeneutic consistency of a structural ontology is a product of a structural representation's ontological components and the mereological relationships between these ontological sub-units: the mapping sentence seminally allows for the depiction of such structure. PMID:27065932

  17. RNA structure alignment by a unit-vector approach.

    Science.gov (United States)

    Capriotti, Emidio; Marti-Renom, Marc A

    2008-08-15

    The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

  18. Matching biomedical ontologies based on formal concept analysis.

    Science.gov (United States)

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

    2018-03-19

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

  19. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Directory of Open Access Journals (Sweden)

    Genki Terashi

    Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

  20. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

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

    Energy Technology Data Exchange (ETDEWEB)

    Uslar, Mathias

    2010-07-01

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

  2. An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies.

    Science.gov (United States)

    Zhang, Guo-Qiang; Xing, Guangming; Cui, Licong

    2018-04-01

    One of the basic challenges in developing structural methods for systematic audition on the quality of biomedical ontologies is the computational cost usually involved in exhaustive sub-graph analysis. We introduce ANT-LCA, a new algorithm for computing all non-trivial lowest common ancestors (LCA) of each pair of concepts in the hierarchical order induced by an ontology. The computation of LCA is a fundamental step for non-lattice approach for ontology quality assurance. Distinct from existing approaches, ANT-LCA only computes LCAs for non-trivial pairs, those having at least one common ancestor. To skip all trivial pairs that may be of no practical interest, ANT-LCA employs a simple but innovative algorithmic strategy combining topological order and dynamic programming to keep track of non-trivial pairs. We provide correctness proofs and demonstrate a substantial reduction in computational time for two largest biomedical ontologies: SNOMED CT and Gene Ontology (GO). ANT-LCA achieved an average computation time of 30 and 3 sec per version for SNOMED CT and GO, respectively, about 2 orders of magnitude faster than the best known approaches. Our algorithm overcomes a fundamental computational barrier in sub-graph based structural analysis of large ontological systems. It enables the implementation of a new breed of structural auditing methods that not only identifies potential problematic areas, but also automatically suggests changes to fix the issues. Such structural auditing methods can lead to more effective tools supporting ontology quality assurance work. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Impact of Information Technology Governance Structures on Strategic Alignment

    Science.gov (United States)

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  4. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    Science.gov (United States)

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

  5. ASH structure alignment package: Sensitivity and selectivity in domain classification

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2007-04-01

    Full Text Available Abstract Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/. Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies.

  6. Crowdsourcing RNA structural alignments with an online computer game.

    Science.gov (United States)

    Waldispühl, Jérôme; Kam, Arthur; Gardner, Paul P

    2015-01-01

    The annotation and classification of ncRNAs is essential to decipher molecular mechanisms of gene regulation in normal and disease states. A database such as Rfam maintains alignments, consensus secondary structures, and corresponding annotations for RNA families. Its primary purpose is the automated, accurate annotation of non-coding RNAs in genomic sequences. However, the alignment of RNAs is computationally challenging, and the data stored in this database are often subject to improvements. Here, we design and evaluate Ribo, a human-computing game that aims to improve the accuracy of RNA alignments already stored in Rfam. We demonstrate the potential of our techniques and discuss the feasibility of large scale collaborative annotation and classification of RNA families.

  7. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

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

    Science.gov (United States)

    Rzhetsky, Andrey; Evans, James A

    2011-09-01

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

  9. Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

    Science.gov (United States)

    Swanson, Larry W

    2018-04-15

    The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  10. Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

    Science.gov (United States)

    2018-01-01

    Abstract The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to “Google Maps” for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3‐D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. PMID:29277900

  11. Structure based alignment and clustering of proteins (STRALCP)

    Science.gov (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  12. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Misra,Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute,Christopher G.; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F.; Musen, Mark A.

    2006-01-23

    The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are: (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. The Center is working toward these objectives by providing tools to develop ontologies and to annotate experimental data, and by developing resources to integrate and relate existing ontologies as well as by creating repositories of biomedical data that are annotated using those ontologies. The Center is providing training workshops in ontology design, development, and usage, and is also pursuing research in ontology evaluation, quality, and use of ontologies to promote scientific discovery. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.

  13. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  14. Alignment between galaxies and large-scale structure

    International Nuclear Information System (INIS)

    Faltenbacher, A.; Li Cheng; White, Simon D. M.; Jing, Yi-Peng; Mao Shude; Wang Jie

    2009-01-01

    Based on the Sloan Digital Sky Survey DR6 (SDSS) and the Millennium Simulation (MS), we investigate the alignment between galaxies and large-scale structure. For this purpose, we develop two new statistical tools, namely the alignment correlation function and the cos(2θ)-statistic. The former is a two-dimensional extension of the traditional two-point correlation function and the latter is related to the ellipticity correlation function used for cosmic shear measurements. Both are based on the cross correlation between a sample of galaxies with orientations and a reference sample which represents the large-scale structure. We apply the new statistics to the SDSS galaxy catalog. The alignment correlation function reveals an overabundance of reference galaxies along the major axes of red, luminous (L ∼ * ) galaxies out to projected separations of 60 h- 1 Mpc. The signal increases with central galaxy luminosity. No alignment signal is detected for blue galaxies. The cos(2θ)-statistic yields very similar results. Starting from a MS semi-analytic galaxy catalog, we assign an orientation to each red, luminous and central galaxy, based on that of the central region of the host halo (with size similar to that of the stellar galaxy). As an alternative, we use the orientation of the host halo itself. We find a mean projected misalignment between a halo and its central region of ∼ 25 deg. The misalignment decreases slightly with increasing luminosity of the central galaxy. Using the orientations and luminosities of the semi-analytic galaxies, we repeat our alignment analysis on mock surveys of the MS. Agreement with the SDSS results is good if the central orientations are used. Predictions using the halo orientations as proxies for central galaxy orientations overestimate the observed alignment by more than a factor of 2. Finally, the large volume of the MS allows us to generate a two-dimensional map of the alignment correlation function, which shows the reference

  15. Information Technology (IT) Strategic Alignment: A Correlational Study between the Impact of IT Governance Structures and IT Strategic Alignment

    Science.gov (United States)

    Asante, Keith K.

    2010-01-01

    This dissertation explored the extent to which Information Technology (IT) strategic alignment are impacted by IT governance structures. The study discusses several strategic alignment and IT governance literature that presents a gap in the literature domain. Subsequent studies researched issues surrounding why organizations are not able to align…

  16. A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).

    Science.gov (United States)

    Bard, Jonathan

    2012-11-01

    This paper describes a new ontology of human developmental anatomy covering the first 49 days [Carnegie stages (CS)1-20], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (AEs) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. Each AE has assigned to it a set of facts of the form , with the relationships including starts_at and ends_at (CSs), part_of (there can be several parents) and is_a (this gives the type of tissue, from an organ system down to one of ~ 80 simple tissues predominantly composed of a single cell kind, which is also specified). Leaf tissues also have a develops_from link to its parent tissue. The ontology includes ~14 000 such facts, which are mainly from the literature and an earlier ontology of human developmental anatomy (EHDAA, now withdrawn). The relationships enable these facts to be integrated into a single, complex hierarchy (or mathematical graph) that was made and can be viewed in the OBO-Edit browser (oboedit.org). Each AE has an EHDAA2 ID that may be useful in an informatics context, while the ontology as a whole can be used for organizing databases of human development. It is also a knowledge resource: a user can trace the lineage of any tissue back to the egg, study the changes in cell phenotype that occur as a tissue develops, and use the structure to add further (e.g. molecular) information. The ontology may be downloaded from www.obofoundry.org. Queries and corrections should be sent to j.bard@ed.ac.uk. © 2012 The Author Journal of Anatomy © 2012 Anatomical Society.

  17. Accelerating large-scale protein structure alignments with graphics processing units

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

    Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

  18. 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…

  19. 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

  20. The mammalian adult neurogenesis gene ontology (MANGO provides a structural framework for published information on genes regulating adult hippocampal neurogenesis.

    Directory of Open Access Journals (Sweden)

    Rupert W Overall

    Full Text Available BACKGROUND: Adult hippocampal neurogenesis is not a single phenotype, but consists of a number of sub-processes, each of which is under complex genetic control. Interpretation of gene expression studies using existing resources often does not lead to results that address the interrelatedness of these processes. Formal structure, such as provided by ontologies, is essential in any field for comprehensive interpretation of existing knowledge but, until now, such a structure has been lacking for adult neurogenesis. METHODOLOGY/PRINCIPAL FINDINGS: We have created a resource with three components 1. A structured ontology describing the key stages in the development of adult hippocampal neural stem cells into functional granule cell neurons. 2. A comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes to the appropriate terms in our ontology. 3. An easy-to-use searchable interface to the resulting database made freely available online. The manuscript presents an overview of the database highlighting global trends such as the current bias towards research on early proliferative stages, and an example gene set enrichment analysis. A limitation of the resource is the current scope of the literature which, however, is growing by around 100 publications per year. With the ontology and database in place, new findings can be rapidly annotated and regular updates of the database will be made publicly available. CONCLUSIONS/SIGNIFICANCE: The resource we present allows relevant interpretation of gene expression screens in terms of defined stages of postnatal neuronal development. Annotation of genes by hand from the adult neurogenesis literature ensures the data are directly applicable to the system under study. We believe this approach could also serve as an example to other fields in a 'bottom-up' community effort complementing the already

  1. Structure, rheology and shear alignment of Pluronic block copolymer mixtures.

    Science.gov (United States)

    Newby, Gemma E; Hamley, Ian W; King, Stephen M; Martin, Christopher M; Terrill, Nicholas J

    2009-01-01

    The structure and flow behaviour of binary mixtures of Pluronic block copolymers P85 and P123 is investigated by small-angle scattering, rheometry and mobility tests. Micelle dimensions are probed by dynamic light scattering. The micelle hydrodynamic radius for the 50/50 mixture is larger than that for either P85 or P123 alone, due to the formation of mixed micelles with a higher association number. The phase diagram for 50/50 mixtures contains regions of cubic and hexagonal phases similar to those for the parent homopolymers, however the region of stability of the cubic phase is enhanced at low temperature and concentrations above 40 wt%. This is ascribed to favourable packing of the mixed micelles containing core blocks with two different chain lengths, but similar corona chain lengths. The shear flow alignment of face-centred cubic and hexagonal phases is probed by in situ small-angle X-ray or neutron scattering with simultaneous rheology. The hexagonal phase can be aligned using steady shear in a Couette geometry, however the high modulus cubic phase cannot be aligned well in this way. This requires the application of oscillatory shear or compression.

  2. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  3. 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....

  4. Survey on Ontology Mapping

    Science.gov (United States)

    Zhu, Junwu

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

  5. Structural re-alignment in an immunologic surface region of ricin A chain

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  6. Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment.

    Science.gov (United States)

    Cao, Hu; Lu, Yonggang

    2017-01-01

    With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities. Accordingly, we propose a new flexible protein structure alignment method based on variable-length AFPs. Compared with other methods, the proposed method possesses three main advantages. First, it is based on variable-length AFPs. The length of each AFP is separately determined to maximally represent a local similar structure fragment, which reduces the number of AFPs. Second, it uses local coordinate systems, which simplify the computation at each step of the expansion of AFPs during the AFP identification. Third, it decreases the number of twists by rewarding the situation where nonconsecutive AFPs share the same transformation in the alignment, which is realized by dynamic programming with an improved transition function. The experimental data show that compared with FlexProt, FATCAT, and FlexSnap, the proposed method can achieve comparable results by introducing fewer twists. Meanwhile, it can generate results similar to those of the FATCAT method in much less running time due to the reduced number of AFPs.

  7. Using structure to explore the sequence alignment space of remote homologs.

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko

    2011-10-01

    Full Text Available Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  8. Using structure to explore the sequence alignment space of remote homologs.

    Science.gov (United States)

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-10-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  9. Structural hierarchy in flow-aligned hexagonally self-organized microphases with parallel polyelectrolytic structures

    NARCIS (Netherlands)

    Ruotsalainen, T; Torkkeli, M; Serimaa, R; Makela, T; Maki-Ontto, R; Ruokolainen, J; ten Brinke, G; Ikkala, O; Mäkelä, Tapio; Mäki-Ontto, Riikka

    2003-01-01

    We report a novel structural hierarchy where a flow-aligned hexagonal self-organized structure is combined with a polyelectrolytic self-organization on a smaller length scale and where the two structures are mutually parallel. Polystyrene-block-poly(4-vinylpyridine) (PS-block-P4VP) is selected with

  10. From Brain Maps to Cognitive Ontologies: Informatics and the Search for Mental Structure.

    Science.gov (United States)

    Poldrack, Russell A; Yarkoni, Tal

    2016-01-01

    A major goal of cognitive neuroscience is to delineate how brain systems give rise to mental function. Here we review the increasingly large role informatics-driven approaches are playing in such efforts. We begin by reviewing a number of challenges conventional neuroimaging approaches face in trying to delineate brain-cognition mappings--for example, the difficulty in establishing the specificity of postulated associations. Next, we demonstrate how these limitations can potentially be overcome using complementary approaches that emphasize large-scale analysis--including meta-analytic methods that synthesize hundreds or thousands of studies at a time; latent-variable approaches that seek to extract structure from data in a bottom-up manner; and predictive modeling approaches capable of quantitatively inferring mental states from patterns of brain activity. We highlight the underappreciated but critical role for formal cognitive ontologies in helping to clarify, refine, and test theories of brain and cognitive function. Finally, we conclude with a speculative discussion of what future informatics developments may hold for cognitive neuroscience.

  11. Biomedical ontologies: toward scientific debate.

    Science.gov (United States)

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

    2011-01-01

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

  12. CO2 and O2 solubility and diffusivity data in food products stored in data warehouse structured by ontology.

    Science.gov (United States)

    Guillard, Valérie; Buche, Patrice; Dibie, Juliette; Dervaux, Stéphane; Acerbi, Filippo; Chaix, Estelle; Gontard, Nathalie; Guillaume, Carole

    2016-06-01

    This data article contains values of oxygen and carbon dioxide solubility and diffusivity measured in various model and real food products. These data are stored in a public repository structured by ontology. These data can be retrieved through the @Web tool, a user-friendly interface to capitalise and query data. The @Web tool is accessible online at http://pfl.grignon.inra.fr/atWeb/.

  13. Web Ontologies to Categorialy Structure Reality: Representations of Human Emotional, Cognitive and Motivational Processes

    Directory of Open Access Journals (Sweden)

    Juan-Miguel eLópez-Gil

    2016-04-01

    Full Text Available This work presents a Web ontology for modeling and representation of the emotional, cognitive and motivational state of online learners, interacting with university systems for distance or blended education. The ontology is understood as a way to provide the required mechanisms to model reality and associate it to emotional responses, but without committing to a particular way of organizing these emotional responses. Knowledge representation for the contributed ontology is performed by using Web Ontology Language (OWL, a semantic web language designed to represent rich and complex knowledge about things, groups of things, and relations between things. OWL is a computational logic-based language such that computer programs can exploit knowledge expressed in OWL and also facilitates sharing and reusing knowledge using the global infrastructure of the Web. The proposed ontology has been tested in the field of Massive Open Online Courses (MOOCs to check if it is capable of representing emotions and motivation of the students in this context of use.

  14. Web Ontologies to Categorialy Structure Reality: Representations of Human Emotional, Cognitive, and Motivational Processes

    Science.gov (United States)

    López-Gil, Juan-Miguel; Gil, Rosa; García, Roberto

    2016-01-01

    This work presents a Web ontology for modeling and representation of the emotional, cognitive and motivational state of online learners, interacting with university systems for distance or blended education. The ontology is understood as a way to provide the required mechanisms to model reality and associate it to emotional responses, but without committing to a particular way of organizing these emotional responses. Knowledge representation for the contributed ontology is performed by using Web Ontology Language (OWL), a semantic web language designed to represent rich and complex knowledge about things, groups of things, and relations between things. OWL is a computational logic-based language such that computer programs can exploit knowledge expressed in OWL and also facilitates sharing and reusing knowledge using the global infrastructure of the Web. The proposed ontology has been tested in the field of Massive Open Online Courses (MOOCs) to check if it is capable of representing emotions and motivation of the students in this context of use. PMID:27199796

  15. 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

  16. 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.

  17. On Algebraic Spectrum of Ontology Evaluation

    OpenAIRE

    Adekoya Adebayo Felix; kinwale Adio Taofiki; Sofoluwe Adetokunbo

    2011-01-01

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

  18. Origin of the Easter Submarine Alignment: morphology and structural lineaments

    Directory of Open Access Journals (Sweden)

    Cristián Rodrigo

    2014-10-01

    Full Text Available The Easter submarine alignment corresponds to a sequence of seamounts and oceanic islands which runs from the Ahu-Umu volcanic fields in the west to its intersection with the Nazca Ridge in the east, with a total length of about 2.900 km and a strike of N85°E. Recent bathymetric compilations that include combined satellite derived and shipboard data (Global Topography and multibeam bathymetric data (from NGDC-NOAA are interpreted both qualitatively and quantitatively by using a morphological analysis, which was comprised of the determination of bathymetric patterns, trends in lineations and structures; height measurements, computation of basal areas and volumes of seamounts, in order to establish clues on the origin of this seamount chain and to establish relationships with the regional tectonics. In the study region 514 seamounts were counted, of which 334 had a basal area less than the reference seamount (Moai. In general, the largest seamounts (>1000 m in height tend to align and to have a larger volume, with an elongation of their bases along the seamount chain. On the other hand, smaller seamounts tend to be distributed more randomly with more circular bases. As a consequence of the morphological analysis, the best possible mechanism that explains the origin of the seamount chain is the existence of a localized hotspot to the west of the Salas y Gómez Island. The corresponding plume would contribute additional magmatic material towards the East Pacific Rise through canalizations, whose secondary branches would feed intermediate volcanoes. It is possible that within the Easter Island region there would be another minor contribution through fractures in the crust, due to the crustal weakening that was produced by the Easter Fracture Zone.

  19. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

  20. Word aligned bitmap compression method, data structure, and apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

  1. Word aligned bitmap compression method, data structure, and apparatus

    Science.gov (United States)

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

  2. Improving model construction of profile HMMs for remote homology detection through structural alignment

    Directory of Open Access Journals (Sweden)

    Zaverucha Gerson

    2007-11-01

    Full Text Available Abstract Background Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. Results We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. Conclusion We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  3. Improving model construction of profile HMMs for remote homology detection through structural alignment.

    Science.gov (United States)

    Bernardes, Juliana S; Dávila, Alberto M R; Costa, Vítor S; Zaverucha, Gerson

    2007-11-09

    Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  4. OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.

    Science.gov (United States)

    Senderov, Viktor; Simov, Kiril; Franz, Nico; Stoev, Pavel; Catapano, Terry; Agosti, Donat; Sautter, Guido; Morris, Robert A; Penev, Lyubomir

    2018-01-18

    The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy. OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses. OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.

  5. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

    2005-01-01

    FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

  6. MultiFarm: A Benchmark for Multilingual Ontology Matching

    NARCIS (Netherlands)

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

    2012-01-01

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

  7. MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

    Science.gov (United States)

    Zhang, Chengxin; Zheng, Wei; Freddolino, Peter L; Zhang, Yang

    2018-03-10

    Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's homology-based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment. Under the stringent benchmark conditions where templates with >30% sequence identity to the query are excluded, MetaGO achieves average F-measures of 0.487, 0.408, and 0.598, for Molecular Function, Biological Process, and Cellular Component, respectively, which are significantly higher than those achieved by other state-of-the-art function annotations methods. Detailed data analysis shows that the major advantage of the MetaGO lies in the new functional homolog detections from partner's homology-based network mapping and structure-based local and global structure alignments, the confidence scores of which can be optimally combined through logistic regression. These data demonstrate the power of using a hybrid model incorporating protein structure and interaction networks to deduce new functional insights beyond traditional sequence homology-based referrals, especially for proteins that lack homologous function templates. The MetaGO pipeline is available at http://zhanglab.ccmb.med.umich.edu/MetaGO/. Copyright © 2018. Published by Elsevier Ltd.

  8. Signalign: An Ontology of DNA as Signal for Comparative Gene Structure Prediction Using Information-Coding-and-Processing Techniques.

    Science.gov (United States)

    Yu, Ning; Guo, Xuan; Gu, Feng; Pan, Yi

    2016-03-01

    Conventional character-analysis-based techniques in genome analysis manifest three main shortcomings-inefficiency, inflexibility, and incompatibility. In our previous research, a general framework, called DNA As X was proposed for character-analysis-free techniques to overcome these shortcomings, where X is the intermediates, such as digit, code, signal, vector, tree, graph network, and so on. In this paper, we further implement an ontology of DNA As Signal, by designing a tool named Signalign for comparative gene structure analysis, in which DNA sequences are converted into signal series, processed by modified method of dynamic time warping and measured by signal-to-noise ratio (SNR). The ontology of DNA As Signal integrates the principles and concepts of other disciplines including information coding theory and signal processing into sequence analysis and processing. Comparing with conventional character-analysis-based methods, Signalign can not only have the equivalent or superior performance, but also enrich the tools and the knowledge library of computational biology by extending the domain from character/string to diverse areas. The evaluation results validate the success of the character-analysis-free technique for improved performances in comparative gene structure prediction.

  9. Improving the accuracy of protein secondary structure prediction using structural alignment

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2006-06-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

  10. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

    Directory of Open Access Journals (Sweden)

    Allen Holder

    2013-11-01

    Full Text Available Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs is robust against both parametric and structural variation.

  11. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

    Science.gov (United States)

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A

    2013-12-01

    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  12. Two obvious intuitions : Ontology-mapping needs background knowledge and approximation

    NARCIS (Netherlands)

    Van Harmelen, Frank

    2007-01-01

    Ontology mapping (or: ontology alignment, or integration) is one of the most active areas the Semantic Web area. An increasing amount of ontologies are becoming available in recent years, and if the Semantic Web is to be taken seriously, the problem of ontology mapping must be solved. Numerous

  13. Web-Beagle: a web server for the alignment of RNA secondary structures.

    Science.gov (United States)

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Structural anisotropy of magnetically aligned single wall carbon nanotube films

    International Nuclear Information System (INIS)

    Smith, B. W.; Benes, Z.; Luzzi, D. E.; Fischer, J. E.; Walters, D. A.; Casavant, M. J.; Schmidt, J.; Smalley, R. E.

    2000-01-01

    Thick films of aligned single wall carbon nanotubes and ropes have been produced by filtration/deposition from suspension in strong magnetic fields. We measured mosaic distributions of rope orientations in the film plane, for samples of different thicknesses. For an ∼1 μm film the full width at half maximum (FWHM) derived from electron diffraction is 25 degree sign -28 degree sign . The FWHM of a thicker film (∼7 μm) measured by x-ray diffraction is slightly broader, 35±3 degree sign . Aligned films are denser than ordinary filter-deposited ones, and much denser than as-grown material. Optimization of the process is expected to yield smaller FWHMs and higher densities. (c) 2000 American Institute of Physics

  15. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng; Naveed, Hammad; Gao, Xin

    2015-01-01

    that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially

  16. High-precision optical systems with inexpensive hardware: a unified alignment and structural design approach

    Science.gov (United States)

    Winrow, Edward G.; Chavez, Victor H.

    2011-09-01

    High-precision opto-mechanical structures have historically been plagued by high costs for both hardware and the associated alignment and assembly process. This problem is especially true for space applications where only a few production units are produced. A methodology for optical alignment and optical structure design is presented which shifts the mechanism of maintaining precision from tightly toleranced, machined flight hardware to reusable, modular tooling. Using the proposed methodology, optical alignment error sources are reduced by the direct alignment of optics through their surface retroreflections (pips) as seen through a theodolite. Optical alignment adjustments are actualized through motorized, sub-micron precision actuators in 5 degrees of freedom. Optical structure hardware costs are reduced through the use of simple shapes (tubes, plates) and repeated components. This approach produces significantly cheaper hardware and more efficient assembly without sacrificing alignment precision or optical structure stability. The design, alignment plan and assembly of a 4" aperture, carbon fiber composite, Schmidt-Cassegrain concept telescope is presented.

  17. Ontological Structures in an Editorial as a Mechanism for the Creation of Meaning in Persuasive Press Texts

    Directory of Open Access Journals (Sweden)

    Topa-Bryniarska Dominika

    2015-09-01

    Full Text Available The aim of this paper is to characterise the manner in which onto- logical structures are created (at the level of text structure and the information layer thereof in press discourse on the example of French newspaper editorials describing political, socio-economic conflicts between the public and the government. Ontological structures and their conceptualisation refer to one of the stages of development of global meaning in the discourse by journalists selecting and categorising the information they wish to provide to their addressees (gate- keeping. Therefore, according to the methodology proposed by Miczka (2002, 2007, 2009, 2011, connecting psycholinguistics (van Dijk & Kintsch, 1983 with the socio-cognitive perspective (Goffman 1974/1986; Langacker, 1987, this pa- per will attempt to describe the discursive mechanisms of creating a common horizon for interpretation in view of persuasive function of the media language (the media declaratives (Nowak & Tokarski 2007, p. 12. The paper proceeds with analysis of editorials on the basis of the concept of Goffman’s framework teamed with Langacker’s cognitive event, as cognitive schemata organise the structure of the experimental frame. It should also be noted that the persuasiveness in the information layer of the utterance forces to ask the question of the responsibility of the media addresser towards the addressee.

  18. Hyperfine-Structure-Induced Depolarization of Impulsively Aligned I2 Molecules

    Science.gov (United States)

    Thomas, Esben F.; Søndergaard, Anders A.; Shepperson, Benjamin; Henriksen, Niels E.; Stapelfeldt, Henrik

    2018-04-01

    A moderately intense 450 fs laser pulse is used to create rotational wave packets in gas phase I2 molecules. The ensuing time-dependent alignment, measured by Coulomb explosion imaging with a delayed probe pulse, exhibits the characteristic revival structures expected for rotational wave packets but also a complex nonperiodic substructure and decreasing mean alignment not observed before. A quantum mechanical model attributes the phenomena to coupling between the rotational angular momenta and the nuclear spins through the electric quadrupole interaction. The calculated alignment trace agrees very well with the experimental results.

  19. Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

    Science.gov (United States)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

    We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.

  20. Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

    Science.gov (United States)

    Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

    2015-01-01

    Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

  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. Intrinsically aligned chemo-mechanical functionalization of twin cantilever structures

    International Nuclear Information System (INIS)

    Toffoli, V; Esch, F; Melli, M; Pozzato, A; Tormen, M; Lazzarino, M; Cataruzza, F; Carrato, S; Scoles, G

    2008-01-01

    Mechanical oscillators became a main focus of research in recent years for potential applications in biomolecule detectors. We recently demonstrated the feasibility of a scheme based on twin cantilevers with a sensitivity down to the single molecule. This approach is extremely promising under the condition that the two terminals of the device can be functionalized with high selectivity and nanometric accuracy by linker molecules. Here we demonstrate a chemo-mechanical method to achieve the intrinsically aligned functionalization of two silicon surfaces, which can be separated by a gap controllable with nanometric precision. The chemical binding of the target molecules in the selected position is obtained through a cycloaddition reaction which exploits the reactivity of the freshly cleaved surfaces that form when the cantilever gap is created. The general validity of this approach is shown by the use in different chemical environments of two compounds with different reactive functional groups.

  3. GOSSIP: a method for fast and accurate global alignment of protein structures.

    Science.gov (United States)

    Kifer, I; Nussinov, R; Wolfson, H J

    2011-04-01

    The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

  4. Audit Validation Using Ontologies

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2015-01-01

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

  5. Biomedicine: an ontological dissection.

    Science.gov (United States)

    Baronov, David

    2008-01-01

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

  6. Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors

    Directory of Open Access Journals (Sweden)

    Robert Preissner

    2009-04-01

    Full Text Available This work presents a generalized approach for the fast structural alignment of thousands of macromolecular structures. The method uses string representations of a macromolecular structure and a hash table that stores n-grams of a certain size for searching. To this end, macromolecular structure-to-string translators were implemented for protein and RNA structures. A query against the index is performed in two hierarchical steps to unite speed and precision. In the first step the query structure is translated into n-grams, and all target structures containing these n-grams are retrieved from the hash table. In the second step all corresponding n-grams of the query and each target structure are subsequently aligned, and after each alignment a score is calculated based on the matching n-grams of query and target. The extendable framework enables the user to query and structurally align thousands of protein and RNA structures on a commodity machine and is available as open source from http://lajolla.sf.net.

  7. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  8. Ontology authoring with Forza

    CSIR Research Space (South Africa)

    Keet, CM

    2014-11-01

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

  9. Using an alignment of fragment strings for comparing protein structures

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Kolodny, Rachel

    2007-01-01

    . RESULTS: Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained...

  10. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

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

  11. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

  12. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

    Science.gov (United States)

    Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

    2016-01-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  13. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

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

  14. Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

    Directory of Open Access Journals (Sweden)

    Junilda Spirollari

    2009-01-01

    Full Text Available Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at http:// datalab.njit.edu/biology/RSpredict.

  15. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Torarinsson, Elfar; Gorodkin, Jan

    2007-01-01

    and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

  16. Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

    International Nuclear Information System (INIS)

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

    2002-01-01

    The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

  17. Considerations in the identification of functional RNA structural elements in genomic alignments

    Directory of Open Access Journals (Sweden)

    Blencowe Benjamin J

    2007-01-01

    Full Text Available Abstract Background Accurate identification of novel, functional noncoding (nc RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. Results We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component was

  18. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2008-04-01

    Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

  19. Local-global alignment for finding 3D similarities in protein structures

    Science.gov (United States)

    Zemla, Adam T [Brentwood, CA

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

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

    Science.gov (United States)

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

    2016-01-01

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

  1. Didactical Ontologies

    Directory of Open Access Journals (Sweden)

    Steffen Mencke, Reiner Dumke

    2008-03-01

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

  2. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

    Science.gov (United States)

    Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

    2016-02-01

    The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  4. Aligning USGS senior leadership structure with the USGS science strategy

    Science.gov (United States)

    ,

    2010-01-01

    The U.S. Geological Survey (USGS) is realigning its management and budget structure to further enhance the work of its science programs and their interdisciplinary focus areas related to the USGS Science Strategy as outlined in 'Facing Tomorrow's Challenges-U.S. Geological Survey Science in the Decade 2007-2017' (U.S. Geological Survey, 2007). In 2007, the USGS developed this science strategy outlining major natural-science issues facing the Nation and focusing on areas where natural science can make a substantial contribution to the well being of the Nation and the world. These areas include global climate change, water resources, natural hazards, energy and minerals, ecosystems, and data integration.

  5. Ontology: A Support Structure for a V-Labs Network: Euronet-Lab

    Directory of Open Access Journals (Sweden)

    Raul Cordeiro Correia

    2012-11-01

    Full Text Available Our propose is to build a network of virtual laboratories, based in a Virtual Closet that will contain all the elements and parts that are needed to build the various experiences available in a v-labs network (that we call Euronet-Lab. To build this complex network we need to find a system that supports effectively this structure. This probably will be a enormous database of v-labs and independent elements, where will be possible sometimes to “recycle” some of the elements. This means “re-use” the same element several times in many experiences. To do this is necessary to have a structure that allows us to have several instances of the same element. It’s important that in our structure and virtual environment we can create several “images” of the same reality and this images can be used simultaneously in different circuits/experiments. This means that we can create several instances of the same element, to be used in different experiences and exercises.

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

    Directory of Open Access Journals (Sweden)

    Rüegg Alexander

    2006-04-01

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

  7. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2017-12-19

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

  8. Design and fabrication of advanced fiber alignment structures for field-installable fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Vervaeke, Michael; Sánchez Martínez, Alberto; Beri, Stefano; Debaes, Christof; Watté, Jan; Thienpont, Hugo

    2012-06-01

    Fiber-To-The-Home (FTTH) networks have been adopted as a potential replacement of traditional electrical connections for the 'last mile' transmission of information at bandwidths over 1Gb/s. However, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field-installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. Novel low-cost structures for bare fiber alignment with outstanding positioning accuracies are strongly desired as they would allow reducing loss beyond the level achievable with ferrule-bore systems. However, the realization of such alignment system is challenging as it should provide sufficient force to position the fiber with sub-micron accuracy required in positioning the fiber. In this contribution we propose, design and prototype a bare-fiber alignment system which makes use of deflectable/compressible micro-cantilevers. Such cantilevers behave as springs and provide self-centering functionality to the structure. Simulations of the mechanical properties of the cantilevers are carried out in order to get an analytical approximation and a mathematical model of the spring constant and stress in the structure. Elastic constants of the order of 104 to 105N/m are found out to be compatible with a proof stress of 70 MPa. Finally a first self-centering structure is prototyped in PMMA using our Deep Proton Writing technology. The spring constants of the fabricated cantilevers are in the range of 4 to 6 × 104N/m and the stress is in the range 10 to 20 MPa. These self-centering structures have the potential to become the basic building blocks for a new generation of field-installable connectors.

  9. Angular momentum-large-scale structure alignments in ΛCDM models and the SDSS

    Science.gov (United States)

    Paz, Dante J.; Stasyszyn, Federico; Padilla, Nelson D.

    2008-09-01

    We study the alignments between the angular momentum of individual objects and the large-scale structure in cosmological numerical simulations and real data from the Sloan Digital Sky Survey, Data Release 6 (SDSS-DR6). To this end, we measure anisotropies in the two point cross-correlation function around simulated haloes and observed galaxies, studying separately the one- and two-halo regimes. The alignment of the angular momentum of dark-matter haloes in Λ cold dark matter (ΛCDM) simulations is found to be dependent on scale and halo mass. At large distances (two-halo regime), the spins of high-mass haloes are preferentially oriented in the direction perpendicular to the distribution of matter; lower mass systems show a weaker trend that may even reverse to show an angular momentum in the plane of the matter distribution. In the one-halo term regime, the angular momentum is aligned in the direction perpendicular to the matter distribution; the effect is stronger than for the one-halo term and increases for higher mass systems. On the observational side, we focus our study on galaxies in the SDSS-DR6 with elongated apparent shapes, and study alignments with respect to the major semi-axis. We study five samples of edge-on galaxies; the full SDSS-DR6 edge-on sample, bright galaxies, faint galaxies, red galaxies and blue galaxies (the latter two consisting mainly of ellipticals and spirals, respectively). Using the two-halo term of the projected correlation function, we find an excess of structure in the direction of the major semi-axis for all samples; the red sample shows the highest alignment (2.7 +/- 0.8per cent) and indicates that the angular momentum of flattened spheroidals tends to be perpendicular to the large-scale structure. These results are in qualitative agreement with the numerical simulation results indicating that the angular momentum of galaxies could be built up as in the Tidal Torque scenario. The one-halo term only shows a significant alignment

  10. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

    2005-01-01

    detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

  11. Binocular contrast-gain control for natural scenes: Image structure and phase alignment.

    Science.gov (United States)

    Huang, Pi-Chun; Dai, Yu-Ming

    2018-05-01

    In the context of natural scenes, we applied the pattern-masking paradigm to investigate how image structure and phase alignment affect contrast-gain control in binocular vision. We measured the discrimination thresholds of bandpass-filtered natural-scene images (targets) under various types of pedestals. Our first experiment had four pedestal types: bandpass-filtered pedestals, unfiltered pedestals, notch-filtered pedestals (which enabled removal of the spatial frequency), and misaligned pedestals (which involved rotation of unfiltered pedestals). Our second experiment featured six types of pedestals: bandpass-filtered, unfiltered, and notch-filtered pedestals, and the corresponding phase-scrambled pedestals. The thresholds were compared for monocular, binocular, and dichoptic viewing configurations. The bandpass-filtered pedestal and unfiltered pedestals showed classic dipper shapes; the dipper shapes of the notch-filtered, misaligned, and phase-scrambled pedestals were weak. We adopted a two-stage binocular contrast-gain control model to describe our results. We deduced that the phase-alignment information influenced the contrast-gain control mechanism before the binocular summation stage and that the phase-alignment information and structural misalignment information caused relatively strong divisive inhibition in the monocular and interocular suppression stages. When the pedestals were phase-scrambled, the elimination of the interocular suppression processing was the most convincing explanation of the results. Thus, our results indicated that both phase-alignment information and similar image structures cause strong interocular suppression. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Ontology-aided Data Fusion (Invited)

    Science.gov (United States)

    Raskin, R.

    2009-12-01

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

  13. Learning Resources Organization Using Ontological Framework

    Science.gov (United States)

    Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

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

  14. L’ontologie des Indivisibles et la structure du continu selon Gautier Burley The ontology of Indivisibles and the structure of continuity according to Walter Burley

    Directory of Open Access Journals (Sweden)

    Alice Lamy

    2011-12-01

    Full Text Available Pour Aristote, sous le rapport de sa composition en parties, le continu est divisible mais sous le rapport de ses limites (point, ligne, surface et profondeur, le continu est indivisible. Walter Burley, comme ses contemporains, a commenté la coexistence problématique de la divisibilité et de l’indivisibilité dans la structure du continu. Bien plus, aux prises avec sa célèbre polémique contre son adversaire Guillaume d’Ockham à propos de l’ontologie de la catégorie de quantité, il admet une structure du continu originale qui semble contenir à la fois des intervalles ou parties divisibles et des points ou indivisibles.For Aristote, concerning its composition in parts, the continuous is divisible but concerning its limits (point, line, surface and depth, the continuous is indivisible. Walter Burley, as his contemporaries, commented on the problematic coexistence of the divisibility and the indivisibility in the structure of the continuous. Much more, battling against his opponent Wilhelm of Ockham about the ontology of the category of quantity, he admits an original structure of continuous who seems to contain at the same time intervals or divisible parts and indivisible points.

  15. Use of ontology structure and Bayesian models to aid the crowdsourcing of ICD-11 sanctioning rules.

    Science.gov (United States)

    Lou, Yun; Tu, Samson W; Nyulas, Csongor; Tudorache, Tania; Chalmers, Robert J G; Musen, Mark A

    2017-04-01

    The International Classification of Diseases (ICD) is the de facto standard international classification for mortality reporting and for many epidemiological, clinical, and financial use cases. The next version of ICD, ICD-11, will be submitted for approval by the World Health Assembly in 2018. Unlike previous versions of ICD, where coders mostly select single codes from pre-enumerated disease and disorder codes, ICD-11 coding will allow extensive use of multiple codes to give more detailed disease descriptions. For example, "severe malignant neoplasms of left breast" may be coded using the combination of a "stem code" (e.g., code for malignant neoplasms of breast) with a variety of "extension codes" (e.g., codes for laterality and severity). The use of multiple codes (a process called post-coordination), while avoiding the pitfall of having to pre-enumerate vast number of possible disease and qualifier combinations, risks the creation of meaningless expressions that combine stem codes with inappropriate qualifiers. To prevent that from happening, "sanctioning rules" that define legal combinations are necessary. In this work, we developed a crowdsourcing method for obtaining sanctioning rules for the post-coordination of concepts in ICD-11. Our method utilized the hierarchical structures in the domain to improve the accuracy of the sanctioning rules and to lower the crowdsourcing cost. We used Bayesian networks to model crowd workers' skills, the accuracy of their responses, and our confidence in the acquired sanctioning rules. We applied reinforcement learning to develop an agent that constantly adjusted the confidence cutoffs during the crowdsourcing process to maximize the overall quality of sanctioning rules under a fixed budget. Finally, we performed formative evaluations using a skin-disease branch of the draft ICD-11 and demonstrated that the crowd-sourced sanctioning rules replicated those defined by an expert dermatologist with high precision and recall

  16. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

    Directory of Open Access Journals (Sweden)

    Jakob H Havgaard

    2007-10-01

    Full Text Available It has become clear that noncoding RNAs (ncRNA play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk.

  17. A Facile Method to Fabricate Anisotropic Hydrogels with Perfectly Aligned Hierarchical Fibrous Structures.

    Science.gov (United States)

    Mredha, Md Tariful Islam; Guo, Yun Zhou; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

    2018-03-01

    Natural structural materials (such as tendons and ligaments) are comprised of multiscale hierarchical architectures, with dimensions ranging from nano- to macroscale, which are difficult to mimic synthetically. Here a bioinspired, facile method to fabricate anisotropic hydrogels with perfectly aligned multiscale hierarchical fibrous structures similar to those of tendons and ligaments is reported. The method includes drying a diluted physical hydrogel in air by confining its length direction. During this process, sufficiently high tensile stress is built along the length direction to align the polymer chains and multiscale fibrous structures (from nano- to submicro- to microscale) are spontaneously formed in the bulk material, which are well-retained in the reswollen gel. The method is useful for relatively rigid polymers (such as alginate and cellulose), which are susceptible to mechanical signal. By controlling the drying with or without prestretching, the degree of alignment, size of superstructures, and the strength of supramolecular interactions can be tuned, which sensitively influence the strength and toughness of the hydrogels. The mechanical properties are comparable with those of natural ligaments. This study provides a general strategy for designing hydrogels with highly ordered hierarchical structures, which opens routes for the development of many functional biomimetic materials for biomedical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    OpenAIRE

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

    2007-01-01

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

  19. Research Update: The electronic structure of hybrid perovskite layers and their energetic alignment in devices

    Directory of Open Access Journals (Sweden)

    Selina Olthof

    2016-09-01

    Full Text Available In recent years, the interest in hybrid organic–inorganic perovskites has increased at a rapid pace due to their tremendous success in the field of thin film solar cells. This area closely ties together fundamental solid state research and device application, as it is necessary to understand the basic material properties to optimize the performances and open up new areas of application. In this regard, the energy levels and their respective alignment with adjacent charge transport layers play a crucial role. Currently, we are lacking a detailed understanding about the electronic structure and are struggling to understand what influences the alignment, how it varies, or how it can be intentionally modified. This research update aims at giving an overview over recent results regarding measurements of the electronic structure of hybrid perovskites using photoelectron spectroscopy to summarize the present status.

  20. A beam-based alignment technique for correction of accelerator structure misalignments

    International Nuclear Information System (INIS)

    Kubo, K.; Raubenheimer, T.O.

    1994-08-01

    This paper describes a method of reducing the transverse emittance dilution in linear colliders due to transverse wakefields arising-from misaligned accelerator structures. The technique is a generalization of the Wake-Free correction algorithm. The structure alignment errors are measured locally by varying the bunch charge and/or bunch length and measuring the change in the beam trajectory. The misalignments can then be corrected by varying the beam trajectory or moving structures. The results of simulations are presented demonstrating the viability of the technique

  1. Developing Learning Materials Using an Ontology of Mathematical Logic

    Science.gov (United States)

    Boyatt, Russell; Joy, Mike

    2012-01-01

    Ontologies describe a body of knowledge and give formal structure to a domain by describing concepts and their relationships. The construction of an ontology provides an opportunity to develop a shared understanding and a consistent vocabulary to be used for a given activity. This paper describes the construction of an ontology for an area of…

  2. Vertically aligned carbon nanotubes/diamond double-layered structure for improved field electron emission stability

    Energy Technology Data Exchange (ETDEWEB)

    Yang, L., E-mail: qiaoqin.yang@mail.usask.ca; Yang, Q.; Zhang, C.; Li, Y.S.

    2013-12-31

    A double-layered nanostructure consisting of a layer of vertically aligned Carbon Nanotubes (CNTs) and a layer of diamond beneath has been synthesized on silicon substrate by Hot Filament Chemical Vapor Deposition. The synthesis was achieved by first depositing a layer of diamond on silicon and then depositing a top layer of vertically aligned CNTs by applying a negative bias on the substrate holder. The growth of CNTs was catalyzed by a thin layer of spin-coated iron nitride. The surface morphology and structure of the CNTs/diamond double-layered structure were characterized by Scanning Electron Microscope, Energy Dispersive X-ray spectrum, and Raman Spectroscopy. Their field electron emission (FEE) properties were measured by KEITHLEY 237 high voltage measurement unit, showing much higher FEE current stability than single layered CNTs. - Highlights: • A new double-layered nanostructure consisting of a layer of vertically aligned CNTs and a layer of diamond beneath has been synthesized by hot filament chemical vapor deposition. • This double-layered structure exhibits superior field electron emission stability. • The improvement of emission stability is due to the combination of the unique properties of diamond and CNTs.

  3. Laser printed glass planar lightwave circuits with integrated fiber alignment structures

    Science.gov (United States)

    Desmet, A.; Radosavljevic, A.; Missinne, J.; Van Thourhout, D.; Van Steenberge, G.

    2018-02-01

    Femtosecond laser inscription allows straightforward manufacturing of glass planar lightwave circuits such as waveguides, interferometers, directional couplers, resonators and more complex structures. Fiber alignment structures are needed to facilitate communication with the glass planar lightwave circuit. In this study, a technique is described to create optical waveguides and alignment structures in the same laser exposure step. Using an industrial ytterbium-doped 1030 nm fiber laser pulses of 400 fs were focused into glass with a 0.4 NA objective causing permanent alteration of the material. Depending on laser parameters this modification allows direct writing of waveguides or the creation of channels after exposing the irradiated volumes to an etchant such as KOH. Writing of channels and waveguides with different laser powers, frequencies, polarisations, stage translation speeds and scan densities were investigated in fused silica and borosilicate glass. Waveguides with controlled dimensions were created, as well as etched U-grooves with a diameter of 126 μm and a sidewall roughness Ra of 255 nm. Cut back measurements were performed giving a waveguide propagation loss of 1.1 dB/cm in borosilicate glass. A coupling loss of 0.7 dB was measured for a transition between the waveguide and standard single mode fiber at 1550 nm, using index matching liquid. The described technique eliminates active alignment requirements and is useful for many applications such as microfluidic sensing, PLCs, fan-out connectors for multicore fibers and quantum optical networks.

  4. Assessment Applications of Ontologies.

    Science.gov (United States)

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

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

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

    Science.gov (United States)

    Martin, Jenny

    2017-10-01

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

  6. Platonic wholes and quantum ontology

    CERN Document Server

    Woszczek, Marek

    2015-01-01

    The subject of the book is a reconsideration of the internalistic model of composition of the Platonic type, more radical than traditional, post-Aristotelian externalistic compositionism, and its application in the field of the ontology of quantum theory. At the centre of quantum ontology is nonseparability. Quantum wholes are atemporal wholes governed by internalistic logic and they are primitive, global physical entities, requiring an extreme relativization of the fundamental notions of mechanics. That ensures quantum theory to be fully consistent with the relativistic causal structure, with

  7. Representation of Gravity-Aligned Scene Structure in Ventral Pathway Visual Cortex.

    Science.gov (United States)

    Vaziri, Siavash; Connor, Charles E

    2016-03-21

    The ventral visual pathway in humans and non-human primates is known to represent object information, including shape and identity [1]. Here, we show the ventral pathway also represents scene structure aligned with the gravitational reference frame in which objects move and interact. We analyzed shape tuning of recently described macaque monkey ventral pathway neurons that prefer scene-like stimuli to objects [2]. Individual neurons did not respond to a single shape class, but to a variety of scene elements that are typically aligned with gravity: large planes in the orientation range of ground surfaces under natural viewing conditions, planes in the orientation range of ceilings, and extended convex and concave edges in the orientation range of wall/floor/ceiling junctions. For a given neuron, these elements tended to share a common alignment in eye-centered coordinates. Thus, each neuron integrated information about multiple gravity-aligned structures as they would be seen from a specific eye and head orientation. This eclectic coding strategy provides only ambiguous information about individual structures but explicit information about the environmental reference frame and the orientation of gravity in egocentric coordinates. In the ventral pathway, this could support perceiving and/or predicting physical events involving objects subject to gravity, recognizing object attributes like animacy based on movement not caused by gravity, and/or stabilizing perception of the world against changes in head orientation [3-5]. Our results, like the recent discovery of object weight representation [6], imply that the ventral pathway is involved not just in recognition, but also in physical understanding of objects and scenes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Single crystalline electronic structure and growth mechanism of aligned square graphene sheets

    Directory of Open Access Journals (Sweden)

    H. F. Yang

    2018-03-01

    Full Text Available Recently, commercially available copper foil has become an efficient and inexpensive catalytic substrate for scalable growth of large-area graphene films for fundamental research and applications. Interestingly, despite its hexagonal honeycomb lattice, graphene can be grown into large aligned square-shaped sheets on copper foils. Here, by applying angle-resolved photoemission spectroscopy with submicron spatial resolution (micro-ARPES to study the three-dimensional electronic structures of square graphene sheets grown on copper foils, we verified the high quality of individual square graphene sheets as well as their merged regions (with aligned orientation. Furthermore, by simultaneously measuring the graphene sheets and their substrate copper foil, we not only established the (001 copper surface structure but also discovered that the square graphene sheets’ sides align with the ⟨110⟩ copper direction, suggesting an important role of copper substrate in the growth of square graphene sheets—which will help the development of effective methods to synthesize high-quality large-size regularly shaped graphene sheets for future applications. This work also demonstrates the effectiveness of micro-ARPES in exploring low-dimensional materials down to atomic thickness and sub-micron lateral size (e.g., besides graphene, it can also be applied to transition metal dichalcogenides and various van der Waals heterostructures

  9. Single crystalline electronic structure and growth mechanism of aligned square graphene sheets

    Science.gov (United States)

    Yang, H. F.; Chen, C.; Wang, H.; Liu, Z. K.; Zhang, T.; Peng, H.; Schröter, N. B. M.; Ekahana, S. A.; Jiang, J.; Yang, L. X.; Kandyba, V.; Barinov, A.; Chen, C. Y.; Avila, J.; Asensio, M. C.; Peng, H. L.; Liu, Z. F.; Chen, Y. L.

    2018-03-01

    Recently, commercially available copper foil has become an efficient and inexpensive catalytic substrate for scalable growth of large-area graphene films for fundamental research and applications. Interestingly, despite its hexagonal honeycomb lattice, graphene can be grown into large aligned square-shaped sheets on copper foils. Here, by applying angle-resolved photoemission spectroscopy with submicron spatial resolution (micro-ARPES) to study the three-dimensional electronic structures of square graphene sheets grown on copper foils, we verified the high quality of individual square graphene sheets as well as their merged regions (with aligned orientation). Furthermore, by simultaneously measuring the graphene sheets and their substrate copper foil, we not only established the (001) copper surface structure but also discovered that the square graphene sheets' sides align with the ⟨110⟩ copper direction, suggesting an important role of copper substrate in the growth of square graphene sheets—which will help the development of effective methods to synthesize high-quality large-size regularly shaped graphene sheets for future applications. This work also demonstrates the effectiveness of micro-ARPES in exploring low-dimensional materials down to atomic thickness and sub-micron lateral size (e.g., besides graphene, it can also be applied to transition metal dichalcogenides and various van der Waals heterostructures)

  10. 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....

  11. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

    DEFF Research Database (Denmark)

    Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2013-01-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

  12. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  13. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    Science.gov (United States)

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  14. Field-aligned plasma-potential structure formed by local electron cyclotron resonance

    International Nuclear Information System (INIS)

    Hatakeyama, Rikizo; Kaneko, Toshiro; Sato, Noriyoshi

    2001-01-01

    The significance of basic experiments on field-aligned plasma-potential structure formed by local electron cyclotron resonance (ECR) is claimed based on the historical development of the investigation on electric double layer and electrostatic potential confinement of open-ended fusion-oriented plasmas. In the presence of a single ECR point in simple mirror-type configurations of magnetic field, a potential dip (thermal barrier) appears around this point, being followed by a subsequent potential hump (plug potential) along a collisionless plasma flow. The observed phenomenon gives a clear-cut physics to the formation of field-aligned plug potential with thermal barrier, which is closely related to the double layer formation triggered by a negative dip. (author)

  15. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

    DEFF Research Database (Denmark)

    Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

    2017-01-01

    . Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

  16. Toxicology ontology perspectives.

    Science.gov (United States)

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

    2012-01-01

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

  17. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul P; Krogh, Anders

    2007-01-01

    function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. AVAILABILITY: Source code available from http://mastr.binf.ku.dk/......MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore......, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction...

  18. XML, Ontologies, and Their Clinical Applications.

    Science.gov (United States)

    Yu, Chunjiang; Shen, Bairong

    2016-01-01

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

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

    Science.gov (United States)

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

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

  20. 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.

  1. 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.

  2. 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.

  3. Hierarchical Analysis of the Omega Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Joslyn, Cliff A.; Paulson, Patrick R.

    2009-12-01

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

  4. Synthesis, structure and magnetic properties of crystallographically aligned CuCr_2Se_4 thin films

    International Nuclear Information System (INIS)

    Esters, Marco; Liebig, Andreas; Ditto, Jeffrey J.; Falmbigl, Matthias; Albrecht, Manfred; Johnson, David C.

    2016-01-01

    We report the low temperature synthesis of highly textured CuCr_2Se_4 thin films using the modulated elemental reactant (MER) method. The structure of CuCr_2Se_4 is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr_2Se_4. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr_2Se_4 synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10"6 erg cm"−"3; shape anisotropy: 1.07 × 10"6 erg cm"−"3), with the easy axis lying out of plane, and a larger magnetic moment (6 μ_B/f.u.) than bulk CuCr_2Se_4. - Highlights: • Crystallographically aligned, phase pure CuCr_2Se_4 were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the direction. • The magnetization is larger than bulk CuCr_2Se_4 or other CuCr_2Se_4 films made to date.

  5. Environmental constraints shaping constituent order in emerging communication systems: Structural iconicity, interactive alignment and conventionalization.

    Science.gov (United States)

    Christensen, Peer; Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    Where does linguistic structure come from? Recent gesture elicitation studies have indicated that constituent order (corresponding to for instance subject-verb-object, or SVO in English) may be heavily influenced by human cognitive biases constraining gesture production and transmission. Here we explore the alternative hypothesis that syntactic patterns are motivated by multiple environmental and social-interactional constraints that are external to the cognitive domain. In three experiments, we systematically investigate different motivations for structure in the gestural communication of simple transitive events. The first experiment indicates that, if participants communicate about different types of events, manipulation events (e.g. someone throwing a cake) and construction events (e.g. someone baking a cake), they spontaneously and systematically produce different constituent orders, SOV and SVO respectively, thus following the principle of structural iconicity. The second experiment shows that participants' choice of constituent order is also reliably influenced by social-interactional forces of interactive alignment, that is, the tendency to re-use an interlocutor's previous choice of constituent order, thus potentially overriding affordances for iconicity. Lastly, the third experiment finds that the relative frequency distribution of referent event types motivates the stabilization and conventionalization of a single constituent order for the communication of different types of events. Together, our results demonstrate that constituent order in emerging gestural communication systems is shaped and stabilized in response to multiple external environmental and social factors: structural iconicity, interactive alignment and distributional frequency. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences

    KAUST Repository

    Roder, Cornelia

    2015-06-19

    The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species’ preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.

  7. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences

    KAUST Repository

    Roder, Cornelia; Bayer, Till; Aranda, Manuel; Kruse, Maren; Voolstra, Christian R.

    2015-01-01

    The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species’ preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.

  8. Conservation success as a function of good alignment of social and ecological structures and processes.

    Science.gov (United States)

    Bodin, Orjan; Crona, Beatrice; Thyresson, Matilda; Golz, Anna-Lea; Tengö, Maria

    2014-10-01

    How to create and adjust governing institutions so that they align (fit) with complex ecosystem processes and structures across scales is an issue of increasing concern in conservation. It is argued that lack of such social-ecological fit makes governance and conservation difficult, yet progress in explicitly defining and rigorously testing what constitutes a good fit has been limited. We used a novel modeling approach and data from case studies of fishery and forest conservation to empirically test presumed relationships between conservation outcomes and certain patterns of alignment of social-ecological interdependences. Our approach made it possible to analyze conservation outcome on a systems level while also providing information on how individual actors are positioned in the complex web of social-ecological interdependencies. We found that when actors who shared resources were also socially linked, conservation at the level of the whole social-ecological system was positively affected. When the scales at which individual actors used resources and the scale at which ecological resources were interconnected to other ecological resources were aligned through tightened feedback loops, conservation outcome was better than when they were not aligned. The analysis of individual actors' positions in the web of social-ecological interdependencies was helpful in understanding why a system has a certain level of social-ecological fit. Results of analysis of positions showed that different actors contributed in very different ways to achieve a certain fit and revealed some underlying difference between the actors, for example in terms of actors' varying rights to access and use different ecological resources. © 2014 Society for Conservation Biology.

  9. 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.

  10. Shock aurora: Field-aligned discrete structures moving along the dawnside oval

    Science.gov (United States)

    Zhou, Xiaoyan; Haerendel, Gerhard; Moen, Jøran I.; Trondsen, Espen; Clausen, Lasse; Strangeway, Robert J.; Lybekk, Bjørn; Lorentzen, Dag A.

    2017-03-01

    Generated by interplanetary shocks or solar wind pressure pulses, shock aurora has transient, global, and dynamic significances and provides a direct manifestation of the solar wind-magnetosphere-ionosphere interaction. As a part of a series of studies of the shock aurora, this paper focuses on the interaction at the morning magnetopause and its auroral manifestation at 06 magnetic local time, where the velocity and magnetic field shears dominate the interaction. Flow shears can generate wave-like structures inside a viscous boundary layer or even larger-scale vortices. These structures couple to the ionosphere via quasi-static field-aligned currents or via kinetic Alfvén waves. Potential drops along field-aligned filaments may be generated accelerating electrons to form auroral manifestations of the structures. A shock aurora event at dawnside is used to test this scenario. The findings include moving auroral streaks/rays that have a vertical profile from red (at 250 km altitude) to purple (at 100 km). The streaks moved antisunward along the poleward boundary of the oval at an ionospheric speed of 3 km s-1. It was mapped to the magnetopause flank at 133 km s-1, which was consistent with the observed speed of the magnetopause surface waves generated by the Kelvin-Helmholtz instability. The calculated field-aligned potential drop using Haerendel's analytic model was 5 kV that reasonably explained the observations. The results support the above scenario and reveal that magnetic and velocity shears at the flanks of the magnetospause may be the main cause of the fast moving shock aurora streaks.

  11. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  12. Methodology for Automatic Ontology Generation Using Database Schema Information

    Directory of Open Access Journals (Sweden)

    JungHyen An

    2018-01-01

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

  13. Global universe anisotropy probed by the alignment of structures in the cosmic microwave background.

    Science.gov (United States)

    Wiaux, Y; Vielva, P; Martínez-González, E; Vandergheynst, P

    2006-04-21

    We question the global universe isotropy by probing the alignment of local structures in the cosmic microwave background (CMB) radiation. The original method proposed relies on a steerable wavelet decomposition of the CMB signal on the sphere. The analysis of the first-year Wilkinson Microwave Anisotropy Probe data identifies a mean preferred plane with a normal direction close to the CMB dipole axis, and a mean preferred direction in this plane, very close to the ecliptic poles axis. Previous statistical anisotropy results are thereby synthesized, but further analyses are still required to establish their origin.

  14. Assembly Test of Elastic Averaging Technique to Improve Mechanical Alignment for Accelerating Structure Assemblies in CLIC

    CERN Document Server

    Huopana, J

    2010-01-01

    The CLIC (Compact LInear Collider) is being studied at CERN as a potential multi-TeV e+e- collider [1]. The manufacturing and assembly tolerances for the required RF-components are important for the final efficiency and for the operation of CLIC. The proper function of an accelerating structure is very sensitive to errors in shape and location of the accelerating cavity. This causes considerable issues in the field of mechanical design and manufacturing. Currently the design of the accelerating structures is a disk design. Alternatively it is possible to create the accelerating assembly from quadrants, which favour the mass manufacturing. The functional shape inside of the accelerating structure remains the same and a single assembly uses less parts. The alignment of these quadrants has been previously made kinematic by using steel pins or spheres to align the pieces together. This method proved to be a quite tedious and time consuming method of assembly. To limit the number of different error sources, a meth...

  15. Optical alignment control of polyimide molecules containing azobenzene in the backbone structure

    International Nuclear Information System (INIS)

    Sakamoto, Kenji; Usami, Kiyoaki; Sasaki, Toru; Kanayama, Takashi; Ushioda, Sukekatsu

    2004-01-01

    Using polarized infrared absorption spectroscopy, we have determined the orientation of the polyimide backbone structure in photo-alignment films for liquid crystals (LC). The polyimide used in this study contains azobenzene in the backbone structure. Photo-alignment treatment was performed on the corresponding polyamic acid film, using a light source of wavelength 340-500 nm. The polyamic acid film (∼16 nm thick) was first irradiated at normal incidence with linearly polarized light (LP-light) of 156 J/cm 2 , and then oblique angle irradiation of unpolarized light (UP-light) was performed in the plane of incidence perpendicular to the polarization direction of the LP-light. The UP-light exposure was varied up to 882 J/cm 2 . We found that the average inclination angle of the polyimide backbone structure, measured from the surface plane, increases almost linearly with UP-light exposure. On the other hand, the in-plane anisotropy induced by the first irradiation with LP-light decreases with the increase of UP-light exposure

  16. Calculation of band alignments and quantum confinement effects in zero- and one-dimensional pseudomorphic structures

    International Nuclear Information System (INIS)

    Yang, M.; Sturm, J.C.; Prevost, J.

    1997-01-01

    The strain field distributions and band lineups of zero-dimensional and one-dimensional strained pseudomorphic semiconductor particles inside a three-dimensional matrix of another semiconductor have been studied. The resulting strain in the particle and the matrix leads to band alignments considerably different from that in the conventional two-dimensional (2D) pseudomorphic growth case. The models are first applied to an ideal spherical and cylindrical Si 1-x Ge x particle in a large Si matrix. In contrast to the 2D case, the band alignments for both structures are predicted to be strongly type II, where the conduction-band edge and the valence-band edge of the Si matrix are both significantly lower than those in the Si 1-x Ge x inclusion, respectively. Band lineups and the lowest electron endash heavy-hole transition energies of a pseudomorphic V-groove Si 1-x Ge x quantum wire inside a large Si matrix have been calculated numerically for different size structures. The photoluminescence energies of a large Si 1-x Ge x V-groove structure on Si will be lower than those of conventional 2D strained Si 1-x Ge x for similar Ge contents. copyright 1997 The American Physical Society

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

    Science.gov (United States)

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

    2013-12-01

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

  18. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    International Nuclear Information System (INIS)

    Frazier, Shane D.; Srubar, Wil V.

    2016-01-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm"3) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  19. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    Energy Technology Data Exchange (ETDEWEB)

    Frazier, Shane D.; Srubar, Wil V., E-mail: wsrubar@colorado.edu

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm{sup 3}) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  20. Quantum physics and relational ontology

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-01

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

  1. Disruption of myoblast alignment by highly motile rhabdomyosarcoma cell in tissue structure.

    Science.gov (United States)

    Li, Menglu; Nagamori, Eiji; Kino-Oka, Masahiro

    2017-02-01

    Rhabdomyosarcoma (RMS) is a highly malignant tumor type of skeletal muscle origin, hallmarked by local invasion. Interaction between invasive tumor cells and normal cells plays a major role in tumor invasion and metastasis. Culturing tumor cells in a three-dimensional (3D) model can translate tumor malignancy relevant cell-cell interaction. To mimic tumor heterogeneity in vitro, a co-culture system consisting of a malignant embryonal rhabdomyosarcoma (ERMS) cell line RD and a normal human skeletal muscle myoblast (HSMM) cell line was established by cell sheet technology. Various ratios of RDs to HSMMs were employed to understand the quantitative effect on intercellular interactions. Disruption of sheet structure was observed in heterogeneous cell sheets having a low ratio of RDs to HSMMs, whereas homogeneous HSMM or RD sheets maintained intact structure. Deeper exploration of dynamic tumor cell behavior inside HSMM sheets revealed that HSMM cell alignment was disrupted by highly motile RDs. This study demonstrated that RMS cells are capable of compromising their surrounding environment through induced decay of HSMMs alignment in a cell-based 3D system. This suggests that muscle disruption might be a major consequence of RMS cell invasion into muscles, which could be a promising target to preventing tumor invasion. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2016-04-01

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

  3. Design and prototyping of self-centering optical single-mode fiber alignment structures

    International Nuclear Information System (INIS)

    Ebraert, Evert; Gao, Fei; Thienpont, Hugo; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2016-01-01

    The European Commission’s goal of providing each European household with at least a 30 Mb s −1 Internet connection by 2020 would be facilitated by a widespread deployment of fibre-to-the-home, which would in turn be sped up by the development of connector essential components, such as high-precision alignment features. Currently, the performance of state-of-the-art physical contact optical fiber connectors is limited by the tolerance on the cladding of standard telecom-grade single-mode fiber (SMF), which is typically smaller than  ±1 μ m. We propose to overcome this limit by developing micro-spring-based self-centering alignment structures (SCAS) for SMF-connectors. We design these alignment structures with robustness and low-cost replication in mind, allowing for large-scale deployment. Both theoretical and finite element analysis (FEA) models are used to determine the optimal dimensions of the beams of which the micro-springs of the SCAS are comprised. Two topologies of the SCAS, consisting of three and four micro-springs respectively, are investigated for two materials: polysulfone (PSU) and polyetherimide (PEI). These materials hold great potential for high-performance fiber connectors while being compatible with low-cost production and with the harsh environmental operation conditions of those connectors. The theory and FEA agree well (<3% difference) for a simple micro-spring. When including a pedestal on the micro-spring (to bring it further away from the fiber) and for shorter spring lengths the agreement worsens. This is due to spring compression effects not being taken into account in our theoretical model. Prototypes are successfully fabricated using deep proton writing and subsequently characterized. The controlled insertion of an SMF in the SCAS is investigated and we determine that a force of 0.11 N is required. The fiber insertion also causes an out-of-plane deformation of the micro-springs in the SCAS of about 7 μ m, which is no

  4. Growth mechanism and internal structure of vertically aligned single-walled carbon nanotubes.

    Science.gov (United States)

    Einarsson, Erik; Kadowaki, Masayuki; Ogura, Kazuaki; Okawa, Jun; Xiang, Rong; Zhang, Zhengyi; Yamamoto, Takahisa; Ikuhara, Yuichi; Maruyama, Shigeo

    2008-11-01

    An in situ optical absorbance technique was used to monitor the growth of vertically aligned single-walled carbon nanotubes (VA-SWNTs) at various temperatures and pressures. The effects of the growth temperature and ethanol pressure on the initial growth rate and catalyst lifetime were investigated. It was found that the ideal pressure for VA-SWNT synthesis changes with the growth temperature, shifting toward higher pressure as the growth temperature increases. It was also found that the growth reaction is first-order below this ideal pressure. Additionally, the internal structure of the VA-SWNT film was observed at different depths into the film by transmission electron microscopy. The absence of large bundles was confirmed, and little change in the structure was observed to a depth of approximately 1 microm.

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

    Science.gov (United States)

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

    2013-01-01

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

  6. Growth and structural discrimination of cortical neurons on randomly oriented and vertically aligned dense carbon nanotube networks

    Directory of Open Access Journals (Sweden)

    Christoph Nick

    2014-09-01

    Full Text Available The growth of cortical neurons on three dimensional structures of spatially defined (structured randomly oriented, as well as on vertically aligned, carbon nanotubes (CNT is studied. Cortical neurons are attracted towards both types of CNT nano-architectures. For both, neurons form clusters in close vicinity to the CNT structures whereupon the randomly oriented CNTs are more closely colonised than the CNT pillars. Neurons develop communication paths via neurites on both nanoarchitectures. These neuron cells attach preferentially on the CNT sidewalls of the vertically aligned CNT architecture instead than onto the tips of the individual CNT pillars.

  7. Towards Agile Ontology Maintenance

    Science.gov (United States)

    Luczak-Rösch, Markus

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

  8. 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.

  9. Knowledge Portals: Ontologies at Work

    OpenAIRE

    Staab, Steffen; Maedche, Alexander

    2001-01-01

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

  10. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  11. Helical structures in vertically aligned dust particle chains in a complex plasma

    Science.gov (United States)

    Hyde, Truell W.; Kong, Jie; Matthews, Lorin S.

    2013-05-01

    Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ2=ω0h/ω0v2 (where ω0h,v are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.85.016406 85, 016406 (2012)].

  12. Practical ontologies for information professionals

    CERN Document Server

    AUTHOR|(CDS)2071712

    2016-01-01

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

  13. Energy band structure tailoring of vertically aligned InAs/GaAsSb quantum dot structure for intermediate-band solar cell application by thermal annealing process.

    Science.gov (United States)

    Liu, Wei-Sheng; Chu, Ting-Fu; Huang, Tien-Hao

    2014-12-15

    This study presents an band-alignment tailoring of a vertically aligned InAs/GaAs(Sb) quantum dot (QD) structure and the extension of the carrier lifetime therein by rapid thermal annealing (RTA). Arrhenius analysis indicates a larger activation energy and thermal stability that results from the suppression of In-Ga intermixing and preservation of the QD heterostructure in an annealed vertically aligned InAs/GaAsSb QD structure. Power-dependent and time-resolved photoluminescence were utilized to demonstrate the extended carrier lifetime from 4.7 to 9.4 ns and elucidate the mechanisms of the antimony aggregation resulting in a band-alignment tailoring from straddling to staggered gap after the RTA process. The significant extension in the carrier lifetime of the columnar InAs/GaAsSb dot structure make the great potential in improving QD intermediate-band solar cell application.

  14. 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

  15. Flux flow and proximity effects in aligned Pb--Cd eutectic lamellar structures

    Energy Technology Data Exchange (ETDEWEB)

    Spencer, C. R.

    1977-09-01

    A high speed directional solidification technique was used to fabricate lamellar Pb-Cd and (Pb-Mg)--(Cd-Mg) superconductor-normal metal composites in which all the lamellae are oriented perpendicular to the broad surface of the sample. These lamellar composites are found to behave like a large number (approximately 1000) of superconducting-normal-superconducting junctions. For the Pb-Cd eutectic system, the critical current densities and critical fields have shown no dependence upon the lamellar periods between 1.0 and 3.1 microns. The critical current density of the aligned lamellar Pb-Cd structures was enhanced approximately 50% when compared to quenched eutectic alloy and to pure Pb. The superconducting transition temperature, T/sub c/, varies inversely with the square of the thickness of the superconducting material as expected from Ginzburg-Landau theory. Upon annealing, the Pb lamellae change from type II to type I superconductivity.

  16. Flux flow and proximity effects in aligned Pb--Cd eutectic lamellar structures

    International Nuclear Information System (INIS)

    Spencer, C.R.

    1977-09-01

    A high speed directional solidification technique was used to fabricate lamellar Pb-Cd and (Pb-Mg)--(Cd-Mg) superconductor-normal metal composites in which all the lamellae are oriented perpendicular to the broad surface of the sample. These lamellar composites are found to behave like a large number (approximately 1000) of superconducting-normal-superconducting junctions. For the Pb-Cd eutectic system, the critical current densities and critical fields have shown no dependence upon the lamellar periods between 1.0 and 3.1 microns. The critical current density of the aligned lamellar Pb-Cd structures was enhanced approximately 50% when compared to quenched eutectic alloy and to pure Pb. The superconducting transition temperature, T/sub c/, varies inversely with the square of the thickness of the superconducting material as expected from Ginzburg-Landau theory. Upon annealing, the Pb lamellae change from type II to type I superconductivity

  17. A novel self-aligned oxygen (SALOX) implanted SOI MOSFET device structure

    Science.gov (United States)

    Tzeng, J. C.; Baerg, W.; Ting, C.; Siu, B.

    The morphology of the novel self-aligned oxygen implanted SOI (SALOX SOI) [1] MOSFET was studied. The channel silicon of SALOX SOI was confirmed to be undamaged single crystal silicon and was connected with the substrate. Buried oxide formed by oxygen implantation in this SALOX SOI structure was shown by a cross section transmission electron micrograph (X-TEM) to be amorphous. The source/drain silicon on top of the buried oxide was single crystal, as shown by the transmission electron diffraction (TED) pattern. The source/drain regions were elevated due to the buried oxide volume expansion. A sharp silicon—silicon dioxide interface between the source/drain silicon and buried oxide was observed by Auger electron spectroscopy (AES). Well behaved n-MOS transistor current voltage characteristics were obtained and showed no I-V kink.

  18. Perspectives on ontology learning

    CERN Document Server

    Lehmann, J

    2014-01-01

    Perspectives on Ontology Learning brings together researchers and practitioners from different communities − natural language processing, machine learning, and the semantic web − in order to give an interdisciplinary overview of recent advances in ontology learning.Starting with a comprehensive introduction to the theoretical foundations of ontology learning methods, the edited volume presents the state-of-the-start in automated knowledge acquisition and maintenance. It outlines future challenges in this area with a special focus on technologies suitable for pushing the boundaries beyond the c

  19. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

    Directory of Open Access Journals (Sweden)

    Michal Brylinski

    2014-09-01

    Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

  20. Determination of material constants of vertically aligned carbon nanotube structures in compressions

    International Nuclear Information System (INIS)

    Li, Yupeng; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-01-01

    Different chemical vapour deposition (CVD) fabrication conditions lead to a wide range of variation in the microstructure and morphologies of carbon nanotubes (CNTs), which actually determine the compressive mechanical properties of CNTs. However, the underlying relationship between the structure/morphology and mechanical properties of CNTs is not fully understood. In this study, we characterized and compared the structural and morphological properties of three kinds of vertically aligned carbon nanotube (VACNT) arrays from different CVD fabrication methods and performed monotonic compressive tests for each VACNT array. The compressive stress–strain responses and plastic deformation were first compared and analyzed with nanotube buckling behaviours. To quantify the compressive properties of the VACNT arrays, a strain density energy function was used to determine their intrinsic material constants. Then, the structural and morphological effects on the quantified material constants of the VACNTs were statistically investigated and analogized to cellular materials with an open-cell model. The statistical analysis shows that density, defect degree, and the moment of inertia of the CNTs are key factors in the improvement of the compressive mechanical properties of VACNT arrays. This approach could allow a model-driven CNT synthesis for engineering their mechanical behaviours. (paper)

  1. 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.

  2. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    Directory of Open Access Journals (Sweden)

    Radhakrishna Bettadapura

    2015-10-01

    Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

  3. Structure and Characterization of Vertically Aligned Single-Walled Carbon Nanotube Bundles

    International Nuclear Information System (INIS)

    Marquez, F.; Morant, C.; Elizalde, E.; Roque-Malherbe, R.; Lopez, V.; Zamora, F.; Domingo, C.

    2010-01-01

    Arrays of vertically aligned single-walled carbon nanotube bundles, SWCNTs, have been synthesized by simple alcohol catalytic chemical vapor deposition process, carried out at 800 degree C. The formed SWCNTs are organized in small groups perpendicularly aligned and attached to the substrate. These small bundles show a constant diameter of ca. 30 nm and are formed by the adhesion of no more than twenty individual SWCNTs perfectly aligned along their length.

  4. A Method for Evaluating and Standardizing Ontologies

    Science.gov (United States)

    Seyed, Ali Patrice

    2012-01-01

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

  5. Manufacturing ontology through templates

    Directory of Open Access Journals (Sweden)

    Diciuc Vlad

    2017-01-01

    Full Text Available The manufacturing industry contains a high volume of knowhow and of high value, much of it being held by key persons in the company. The passing of this know-how is the basis of manufacturing ontology. Among other methods like advanced filtering and algorithm based decision making, one way of handling the manufacturing ontology is via templates. The current paper tackles this approach and highlights the advantages concluding with some recommendations.

  6. The Electronic Notebook Ontology

    OpenAIRE

    Chalk, Stuart

    2016-01-01

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

  7. Ontology Update in the Cognitive Model of Ontology Learning

    Directory of Open Access Journals (Sweden)

    Zhang De-Hai

    2016-01-01

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

  8. Poly(vinyl alcohol)/cellulose nanofibril hybrid aerogels with an aligned microtubular porous structure and their composites with polydimethylsiloxane

    Science.gov (United States)

    Tianliang Zhai; Qifeng Zheng; Zhiyong Cai; Lih-Sheng Turng; Hesheng Xia; Shaoqin Gong

    2015-01-01

    Superhydrophobic poly(vinyl alcohol) (PVA)/ cellulose nanofibril (CNF) aerogels with a unidirectionally aligned microtubular porous structure were prepared using a unidirectional freeze-drying process, followed by the thermal chemical vapor deposition of methyltrichlorosilane. The silanized aerogels were characterized using various techniques including scanning...

  9. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.

    2013-01-01

    Roč. 12, č. 2 (2013), s. 305-319 ISSN 1617-416X R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : 2D structure * 2D mask * alignment Subject RIV: EF - Botanics Impact factor: 1.543, year: 2013

  10. Replication of self-centering optical fiber alignment structures using hot embossing

    Science.gov (United States)

    Ebraert, Evert; Wissmann, Markus; Barié, Nicole; Guttmann, Markus; Schneider, Marc; Kolew, Alexander; Worgull, Matthias; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

    2016-04-01

    With the demand for broadband connectivity on the rise due to various services like video-on-demand and cloud computing becoming more popular, the need for better connectivity infrastructure is high. The only future- proof option to supply this infrastructure is to deploy "fiber to the home" (FTTH) networks. One of the main difficulties with the deployment of FTTH is the vast amount of single-mode fiber (SMF) connections that need to be made. Hence there is a strong need for components which enable high performance, robust and easy-to- use SMF connectors. Since large-scale deployment is the goal, these components should be mass-producible at low cost. We discuss a rapid prototyping process on the basis of hot embossing replication of a self-centering alignment system (SCAS) based on three micro-springs, which can position a SMF independently of its diameter. This is beneficial since there is a fabrication tolerance of up to +/-1 μm on a standard G.652 SMF's diameter that can lead to losses if the outer diameter is used as a reference for alignment. The SCAS is first prototyped with deep proton writing (DPW) in polymethylmethacrylate (PMMA) after which it is glued to a copper substrate with an adhesive. Using an electroforming process, a nickel block is grown over the PMMA prototype followed by mechanical finishing to fabricate a structured nickel mould insert. Even though the mould insert shows non- ideal and rounded features it is used to create PMMA replicas of the SCAS by means of hot embossing. The SCAS possesses a central opening in which a bare SMF can be clamped, which is designed with a diameter of 121 μm. PMMA replicas are dimensionally characterized using a multisensor coordinate measurement machine and show a central opening diameter of 128.3 +/- 2.8 μm. This should be compared to the central opening diameter of the DPW prototype used for mould formation which was measured to be 120.5 μm. This shows that the electroforming and subsequent replication

  11. Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules

    International Nuclear Information System (INIS)

    Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

    2009-01-01

    We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

  12. Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships.

    Science.gov (United States)

    Manda, Prashanti; McCarthy, Fiona; Bridges, Susan M

    2013-10-01

    The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular bio-ontologies used for describing gene product characteristics. GO annotation data containing terms from multiple sub-ontologies and at different levels in the ontologies is an important source of implicit relationships between terms from the three sub-ontologies. Data mining techniques such as association rule mining that are tailored to mine from multiple ontologies at multiple levels of abstraction are required for effective knowledge discovery from GO annotation data. We present a data mining approach, Multi-ontology data mining at All Levels (MOAL) that uses the structure and relationships of the GO to mine multi-ontology multi-level association rules. We introduce two interestingness measures: Multi-ontology Support (MOSupport) and Multi-ontology Confidence (MOConfidence) customized to evaluate multi-ontology multi-level association rules. We also describe a variety of post-processing strategies for pruning uninteresting rules. We use publicly available GO annotation data to demonstrate our methods with respect to two applications (1) the discovery of co-annotation suggestions and (2) the discovery of new cross-ontology relationships. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Embedded Aligned Carbon Nanotube Sheets for Strain and Damage sensing in Composite Structures

    Science.gov (United States)

    Aly, Karim Aly Abdelomoaty Elsayed

    The world demand for fiber reinforced composite materials has been steadily increasing because of the widespread adoption of this class of material in many markets. The automotive, aerospace, marine and energy sectors account for a large percentage of this grow. Outstanding fatigue performance, high specific stiffness and strength, and low density are among the most important properties that fiber reinforced polymer composites offer. Furthermore, their properties can be tailored to meet the specific needs of the final applications. However, this class of material is composed of multiple layers of inhomogeneous and anisotropic constituents, i.e. fibers and matrix. Therefore, this laminated nature make the composite material prone to intrinsic damage including interfacial debonding and delamination and their strength and failure are dependent on the fiber architecture and direction of the applied stresses. Consequently, it is of prime importance to monitor the health of these structures. New and improved methods for early detection of damage and structural health monitoring of composite materials may allow for enhanced reliability, lifetime and performance while minimizing maintenance time during a composite part's service life. Over the last few decades different non-destructive methods and materials have been investigated for use as strain sensors. Since the discovery of carbon nanotubes (CNTs), they have attracted much research interest due to their superior electrical, thermal and mechanical properties as well as their high aspect ratio. In this context, CNTs have been used in the recent years to enable sensing capabilities. In this dissertation, the usage of CNTs for performing strain and damage sensing in composites is evaluated. This was enabled by embedding aligned sheets of two millimeters long, interconnected CNTs into laminated structures that were then subjected to different forms of mechanical loading. The localization of the CNT sheets inside the host

  14. Magnet Cycles and Stability Periods of the CMS Structures from 2008 to 2013 as Observed by the Link Alignment System

    International Nuclear Information System (INIS)

    Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M.I.; Molinero, A.; Navarrete, J.; Oller, J.C.

    2015-01-01

    In this document Magnet Cycles and Stability Periods of the CMS Experiment are studied with the recorded Alignment Link System data along the 2008 to 2013 years of operation. The motions of the mechanical structures due to the magnetic field forces are studied including an in-depth analysis of the relative distance between the endcap structures and the central Tracker body during the Stability Periods to verify the mechanical stability of the detector during the physics data taking.

  15. The influence of polysilane chemical structure on optical properties, rubbed film morphology and LC alignment

    Directory of Open Access Journals (Sweden)

    M. Soroceanu

    2015-05-01

    Full Text Available Polysilane films were prepared by the drop casting method and their optical and morphological properties have been analyzed in order to investigate their suitability as alignment layers for nematic molecules. The samples do not absorb the radiations in the visible domain, particularly those containing methylhydrosilyl units, and present a transmittance of about 90% starting from 390 to 1100 nm. The optical band-gap is higher than 3.26 eV for all polysilanes indicating a low probability of optical absorption processes in the visible range. The morphology of the pristine samples shows isotropically distributed granular formations. The polymer surface was oriented by rubbing with two types of velvet: one with short fibers and the other with long fibers. The latter generates higher surface anisotropy, as shown by the reduction of the surface texture direction index values. The presence of methylhydrosilyl units allows a denser packing of the polymer structure and thus finer surface periodicities, leading to better orientation of the nematic molecules on the polysilane surface.

  16. Characteristics of electron cyclotron waves creating field-aligned and transverse plasma-potential structures

    International Nuclear Information System (INIS)

    Takahashi, K; Kaneko, T; Hatakeyama, R; Fukuyama, A

    2009-01-01

    Characteristics of electromagnetic waves of azimuthal mode number m = ±1 are investigated experimentally, analytically and numerically when the waves triggering the field-aligned and transverse plasma-potential structure modification near an electron cyclotron resonance (ECR) point are injected into an inhomogeneously magnetized plasma with high-speed ion flow. The waves of m = +1 and -1 modes generate an electric double layer near the ECR point at the radially central and peripheral areas of the plasma column, respectively, and the transverse electric fields are consequently formed. At these areas the waves have a right-handed polarization and are absorbed through the ECR mechanism, where the experimental and analytical results do show the polarization reversal along the radial axis. The numerical results by plasma analysis by finite element method (FEM)/wave analysis by FEM (PAF/WF) code show that the wave-absorption area is localized at the radially central and peripheral areas for m = +1 and -1 mode waves, respectively, being consistent with the experimental and analytical ones.

  17. 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

  18. Interpreting XML documents via an RDF schema ontology

    NARCIS (Netherlands)

    Klein, Michel

    2002-01-01

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

  19. CAS-ATLID (co-alignment sensor of ATLID instrument) thermo-structural design and performance

    Science.gov (United States)

    Moreno, Javier; Serrano, Javier; González, David; Rodríguez, Gemma; Manjón, Andrés.; Vásquez, Eloi; Carretero, Carlos; Martínez, Berta

    2017-11-01

    This paper describes the main thermo-mechanical design features and performances of the Co-Alignment Sensor (CAS) developed by LIDAX and CRISA under ESA program with AIRBUS Defence and Space as industry prime.

  20. Unintended consequences of existential quantifications in biomedical ontologies

    Directory of Open Access Journals (Sweden)

    Boeker Martin

    2011-11-01

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

  1. Revival structures of linear molecules in a field-free alignment condition as probed by high-order harmonic generation

    International Nuclear Information System (INIS)

    Lee, G. H.; Kim, H. T.; Park, J. Y.; Nam, C. H.; Kim, T. K.; Lee, J. H.; Ihee, H.

    2006-01-01

    Revival structures (rotational coherence) of three linear molecules (N 2 , O 2 , and CO 2 ) in a field free alignment condition have been investigated using high-order harmonic generation. The harmonic yields of these molecules were measured in a pump-probe manner by using a weak femtosecond (fs) laser pulse for field-free alignment of molecules and another intense fs laser pulse for harmonic generation. The harmonic intensities from 23rd to 29th order with respect to the time delay between the pump and the probe pulses showed revival structures in the condition of a field-free alignment of molecules. While the revival structure of a N 2 molecule had one-fourth the period of the full revival time and different degrees of modulation among different fractional revival times, the revival structures of O 2 and CO 2 molecules showed one-eighth the periods of the full revival time and similar degrees of modulation among all fractional revival times. The revival structures could be interpreted in terms of the nature of the highest occupied molecular orbital and the total nuclear spin.

  2. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  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. 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.

  5. 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.

  6. The Cognitive Paradigm Ontology: Design and Application

    Science.gov (United States)

    Laird, Angela R.

    2013-01-01

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

  7. 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 ...

  8. Ontology and medical diagnosis.

    Science.gov (United States)

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

    2012-03-01

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

  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. 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

  11. ONTOLOGY IN PHARMACY

    Directory of Open Access Journals (Sweden)

    L. Yu. Babintseva

    2015-05-01

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

  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. Are institutional missions aligned with journal-based or document-based disciplinary structures?

    Energy Technology Data Exchange (ETDEWEB)

    Klavans, R.; Boyack, K.W.

    2016-07-01

    Missions represent the underlying purpose of an institution. These missions can be focused (finding a cure for cancer) or diverse (providing all health services to a local population). They might be aimed at basic research (finding new sub-atomic particles) or very applied (forecasting tomorrow’s weather). Missions can be extremely practical (building i-phones) or abstract (creating maps of scientific inquiry). Our primary focus is on those institutions that are also contributing to society’s knowledge about scientific and technical phenomena. The publications of these institutions are, to some degree, an implicit statement of their mission. Institutions focusing on a cure for cancer will publish articles associated with cancer, while hospitals will publish in a diverse set of medical specialties. Institutions focused on subatomic particles publish in specialized physics journals. While the publication profile of an institution is obviously not the same as an institution’s mission, it is typically consistent with its mission. In this study we analyze the publication profiles of over 4400 institutions using Scopus data to determine if their institutional missions are best explained using a journal-based classification system or a document-based classification system. The structure of this article is as follows. The background section places this work in the context of two streams of research – the accuracies of different document classification systems, and the effect of different national contexts (specifically wealth, health and democracy) on science systems and their impact. We then describe our data and methods before addressing two questions: Do the missions of certain types of institutions align with journal-based or article-based disciplines, and does this vary with national context (wealth, health and democracy). We conclude with a discussion of limitations and possible areas for further investigation. (Author)

  14. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

    Science.gov (United States)

    Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

    2009-06-01

    Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

  15. Application of Ontology Technology in Health Statistic Data Analysis.

    Science.gov (United States)

    Guo, Minjiang; Hu, Hongpu; Lei, Xingyun

    2017-01-01

    Research Purpose: establish health management ontology for analysis of health statistic data. Proposed Methods: this paper established health management ontology based on the analysis of the concepts in China Health Statistics Yearbook, and used protégé to define the syntactic and semantic structure of health statistical data. six classes of top-level ontology concepts and their subclasses had been extracted and the object properties and data properties were defined to establish the construction of these classes. By ontology instantiation, we can integrate multi-source heterogeneous data and enable administrators to have an overall understanding and analysis of the health statistic data. ontology technology provides a comprehensive and unified information integration structure of the health management domain and lays a foundation for the efficient analysis of multi-source and heterogeneous health system management data and enhancement of the management efficiency.

  16. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

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

    2011-08-11

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

  17. 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.

  18. 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.

  19. Ontology-Based Model Of Firm Competitiveness

    Science.gov (United States)

    Deliyska, Boryana; Stoenchev, Nikolay

    2010-10-01

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

  20. Survey Relationship between IT-business Alignment and Business Performance: Using Structural Equation Model

    Directory of Open Access Journals (Sweden)

    amir manian

    2009-09-01

    Full Text Available In spite of importance of IT deployment, nowadays in many organizations we are witness of appearing problems related to dissatisfaction of business needs due to high investment in the field of IT. The fervent debate concerning IT productivity–or lack of such productivity- named productivity paradox persuade us to survey relationship between IT–business alignment and business performance. The purpose of this research is to investigate whether IT-business alignment could have a decisive influence on their performance in IT-base firms by adopting a contingency theory perspective and operationalizing the fit systemically. Also to measure organizational performance, we adopt BSC framework which is not applied in this matter yet. Finally, this paper will explore the notion that alignment between business and IT is the key to achieving improved business performance through IT.

  1. 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 ...

  2. 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…

  3. Asian Educational Discourse: Construction of Ontological Security

    Science.gov (United States)

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

    2018-01-01

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

  4. 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

  5. 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.

  6. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

    Directory of Open Access Journals (Sweden)

    Lei Hua

    Full Text Available RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

  7. 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...

  8. Aligning the unalignable: bacteriophage whole genome alignments.

    Science.gov (United States)

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  9. From Patient Discharge Summaries to an Ontology for Psychiatry.

    Science.gov (United States)

    Richard, Marion; Aimé, Xavier; Jaulent, Marie-Christine; Krebs, Marie-Odile; Charlet, Jean

    2017-01-01

    Psychiatry aims at detecting symptoms, providing diagnoses and treating mental disorders. We developed ONTOPSYCHIA, an ontology for psychiatry in three modules: social and environmental factors of mental disorders, mental disorders, and treatments. The use of ONTOPSYCHIA, associated with dedicated tools, will facilitate semantic research in Patient Discharge Summaries (PDS). To develop the first module of the ontology we propose a PDS text analysis in order to explicit psychiatry concepts. We decided to set aside classifications during the construction of the modu le, to focus only on the information contained in PDS (bottom-up approach) and to return to domain classifications solely for the enrichment phase (top-down approach). Then, we focused our work on the development of the LOVMI methodology (Les Ontologies Validées par Méthode Interactive - Ontologies Validated by Interactive Method), which aims to provide a methodological framework to validate the structure and the semantic of an ontology.

  10. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

    Science.gov (United States)

    Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2012-02-15

    We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

  11. The representation of heart development in the gene ontology.

    Science.gov (United States)

    Khodiyar, Varsha K; Hill, David P; Howe, Doug; Berardini, Tanya Z; Tweedie, Susan; Talmud, Philippa J; Breckenridge, Ross; Bhattarcharya, Shoumo; Riley, Paul; Scambler, Peter; Lovering, Ruth C

    2011-06-01

    An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. Copyright © 2011

  12. The Representation of Heart Development in the Gene Ontology

    Science.gov (United States)

    Khodiyar, Varsha K.; Hill, David P.; Howe, Doug; Berardini, Tanya Z.; Tweedie, Susan; Talmud, Philippa J.; Breckenridge, Ross; Bhattarcharya, Shoumo; Riley, Paul; Scambler, Peter; Lovering, Ruth C.

    2012-01-01

    An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development and aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. PMID:21419760

  13. Uberon, an integrative multi-species anatomy ontology

    Science.gov (United States)

    2012-01-01

    We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

  14. PAV ontology: provenance, authoring and versioning.

    Science.gov (United States)

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

    2013-11-22

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

  15. Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

    Directory of Open Access Journals (Sweden)

    Nicola Mulder

    2016-06-01

    The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.

  16. Design of Electrically Conductive Structural Composites by Modulating Aligned CVD-Grown Carbon Nanotube Length on Glass Fibers.

    Science.gov (United States)

    He, Delong; Fan, Benhui; Zhao, Hang; Lu, Xiaoxin; Yang, Minhao; Liu, Yu; Bai, Jinbo

    2017-01-25

    Function-integration in glass fiber (GF) reinforced polymer composites is highly desired for developing lightweight structures and devices with improved performance and structural health monitoring. In this study, homogeneously aligned carbon nanotube (CNT) shell was in situ grafted on GF by chemical vapor deposition (CVD). It was demonstrated that the CNT shell thickness and weight fraction can be modulated by controlling the CVD conditions. The obtained hierarchical CNTs-GF/epoxy composites show highly improved electrical conductivity and thermo-mechanical and flexural properties. The composite through-plane and in-plane electrical conductivities increase from a quasi-isolator value to ∼3.5 and 100 S/m, respectively, when the weight fraction of CNTs grafted on GF fabric varies from 0% to 7%, respectively. Meanwhile, the composite storage modulus and flexural modulus and strength improve as high as 12%, 21%, and 26%, respectively, with 100% retention of the glass transition temperature. The reinforcing mechanisms are investigated by analyzing the composite microstructure and the interfacial adhesion and wetting properties of CNTs-GF hybrids. Moreover, the specific damage-related resistance variation characteristics could be employed to in situ monitor the structural health state of the composites. The outstanding electrical and structural properties of the CNTs-GF composites were due to the specific interfacial and interphase structures created by homogeneously grafting aligned CNTs on each GF of the fabric.

  17. Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

    Science.gov (United States)

    Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

    2013-09-01

    Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

  18. Completeness, supervenience and ontology

    International Nuclear Information System (INIS)

    Maudlin, Tim W E

    2007-01-01

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

  19. Completeness, supervenience and ontology

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-23

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

  20. ER2OWL: Generating OWL Ontology from ER Diagram

    Science.gov (United States)

    Fahad, Muhammad

    Ontology is the fundamental part of Semantic Web. The goal of W3C is to bring the web into (its full potential) a semantic web with reusing previous systems and artifacts. Most legacy systems have been documented in structural analysis and structured design (SASD), especially in simple or Extended ER Diagram (ERD). Such systems need up-gradation to become the part of semantic web. In this paper, we present ERD to OWL-DL ontology transformation rules at concrete level. These rules facilitate an easy and understandable transformation from ERD to OWL. The set of rules for transformation is tested on a structured analysis and design example. The framework provides OWL ontology for semantic web fundamental. This framework helps software engineers in upgrading the structured analysis and design artifact ERD, to components of semantic web. Moreover our transformation tool, ER2OWL, reduces the cost and time for building OWL ontologies with the reuse of existing entity relationship models.

  1. Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

    2010-01-01

    of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

  2. LOGISTICS OPTIMIZATION USING ONTOLOGIES

    OpenAIRE

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

    2014-01-01

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

  3. Ontology evolution in physics

    OpenAIRE

    Chan, Michael

    2013-01-01

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

  4. 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

  5. Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

    Science.gov (United States)

    Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

    2008-09-01

    A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

  6. Myristoylation as a general method for immobilization and alignment of soluble proteins for solid-state NMR structural studies

    International Nuclear Information System (INIS)

    Mesleh, M.F.; Valentine, K.G.; Opella, S.J.; Louis, J.M.; Gronenborn, A.M.

    2003-01-01

    N-terminal myristoylation of the immunoglobulin-binding domain of protein G (GB1) from group G Streptococcus provides the means to bind the protein to aligned phospholipid bilayers for solid-state NMR structural studies. The myristoylated protein is immobilized by its interactions with bilayers, and the sample alignment enables orientationally dependent 15 N chemical shifts and 1 H- 15 N-dipolar couplings to be measured. Spectra calculated for the average solution NMR structure of the protein at various orientations with respect to the magnetic field direction were compared to the experimental spectrum. The best fit identified the orientation of the myristoylated protein on the lipid bilayers, and demonstrated that the protein adopts a similar structure in both its myristoylated and non-myristoylated forms, and that the structure is not grossly distorted by its interaction with the phosholipid bilayer surface or by its location in the restricted aqueous space between bilayer leaflets. The protein is oriented such that its charged sides face the phosphatidylcholine headgroups of the lipids with the single amphiphilic helix running parallel to the bilayer surface

  7. Feasibility of automated foundational ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2014-11-01

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

  8. 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…

  9. Ontology Design Patterns for Combining Pathology and Anatomy: Application to Study Aging and Longevity in Inbred Mouse Strains

    KAUST Repository

    Alghamdi, Sarah M.

    2018-05-13

    In biomedical research, ontologies are widely used to represent knowledge as well as to annotate datasets. Many of the existing ontologies cover a single type of phenomena, such as a process, cell type, gene, pathological entity or anatomical structure. Consequently, there is a requirement to use multiple ontologies to fully characterize the observations in the datasets. Although this allows precise annotation of different aspects of a given dataset, it limits our ability to use the ontologies in data analysis, as the ontologies are usually disconnected and their combinations cannot be exploited. Motivated by this, here we present novel ontology design methods for combining pathology and anatomy concepts. To this end, we use a dataset of mouse models which has been characterized through two ontologies: one of them is the mouse pathology ontology (MPATH) covering pathological lesions while the other is the mouse anatomy ontology (MA) covering the anatomical site of the lesions. We propose four novel ontology design patterns for combining these ontologies, and use these patterns to generate four ontologies in a data-driven way. To evaluate the generated ontologies, we utilize these in ontology-based data analysis, including ontology enrichment analysis and computation of semantic similarity. We demonstrate that there are significant differences between the four ontologies in different analysis approaches. In addition, when using semantic similarity to confirm the hypothesis that genetically identical mice should develop more similar diseases, the generated combined ontologies lead to significantly better analysis results compared to using each ontology individually. Our results reveal that using ontology design patterns to combine different facets characterizing a dataset can improve established analysis methods.

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

    Directory of Open Access Journals (Sweden)

    Wasila M Dahdul

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

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

    Science.gov (United States)

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

    2012-01-01

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

  12. A Unified Anatomy Ontology of the Vertebrate Skeletal System

    Science.gov (United States)

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

    2012-01-01

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

  13. 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.

  14. Electronic structure of indium-tungsten-oxide alloys and their energy band alignment at the heterojunction to crystalline silicon

    Science.gov (United States)

    Menzel, Dorothee; Mews, Mathias; Rech, Bernd; Korte, Lars

    2018-01-01

    The electronic structure of thermally co-evaporated indium-tungsten-oxide films is investigated. The stoichiometry is varied from pure tungsten oxide to pure indium oxide, and the band alignment at the indium-tungsten-oxide/crystalline silicon heterointerface is monitored. Using in-system photoelectron spectroscopy, optical spectroscopy, and surface photovoltage measurements, we show that the work function of indium-tungsten-oxide continuously decreases from 6.3 eV for tungsten oxide to 4.3 eV for indium oxide, with a concomitant decrease in the band bending at the hetero interface to crystalline silicon than indium oxide.

  15. Investigating Knee Alignment and Foot Structure in Futsal Players with and without Hamstring Shortness

    Directory of Open Access Journals (Sweden)

    Homan Minoonejad

    2016-09-01

    Methods: In this descriptive - comparative study, 30 men athlete (18- 25 years were recruited. They were assigned into two groups of 15 subjects with and without hamstring shortness. The hamstring shortness, knee and foot alignment were respectively measured by the goniometer, the ruler and caliper. After checking the normality of the data, (with Shapiro-Wilk test independent samples t-test, were used to analyze of data at a significance level of P 0.05. Conclusion: It seems that, navicular drop is not common among athletes with hamstring shortness.

  16. 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.

  17. 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

  18. Ontology for cell-based geographic information

    Science.gov (United States)

    Zheng, Bin; Huang, Lina; Lu, Xinhai

    2009-10-01

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

  19. Collimated-hole structures as efficient differential pumping barrier, one-way valve and tool for aligning Penning traps

    International Nuclear Information System (INIS)

    Kluge, H.-Jürgen; Block, Michael; Herfurth, Frank

    2011-01-01

    A collimated-hole structure consists of a very large number of parallel channels which have each a very small diameter and are closely packed together. Such devices, installed in vacuum systems allow one to separate regions of very different gas pressures. A collimated-hole structure has high transmission for a directed ion beam with low emittance but a very low conductance for rest gas atoms or molecules exhibiting random walk. Therefore it is proposed to use such a structure as one-way valve and/or efficient differential pumping barrier in set-ups using Penning traps. Furthermore, these devices might be very useful to align the axis of a Penning trap with the direction of the magnetic field lines which is essential to avoid systematic uncertainties in high-accuracy mass spectroscopy.

  20. 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...

  1. Application of neuroanatomical ontologies for neuroimaging data annotation

    Directory of Open Access Journals (Sweden)

    Jessica A Turner

    2010-06-01

    Full Text Available The annotation of functional neuroimaging results for data sharing and reuse is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus. This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural and morphological labeling schemas. We annotated a large functional neuroimaging dataset with terms from the ontology and applied a reasoning engine to analyze this dataset in conjunction with the ontology, and achieved successful inferences from the most specific level (e.g., how many subjects showed activation in a sub-part of the middle frontal gyrus to more general (how many activations were found in areas connected via a known white matter tract?. In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes. This neuranatomical ontology is publicly available as a view of FMA at the Bioportal website at http://rest.bioontology.org/bioportal/ontologies/download/10005. The ontological encoding of anatomic knowledge can be exploited by computer reasoning engines to make inferences about neuroanatomical relationships described in imaging datasets using different terminologies. This approach could ultimately enable knowledge discovery from large, distributed fMRI studies or medical record mining.

  2. 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

  3. Low-temperature growth of aligned ZnO nanorods: effect of annealing gases on the structural and optical properties.

    Science.gov (United States)

    Umar, Ahmad; Hahn, Yoon-Bong; Al-Hajry, A; Abaker, M

    2014-06-01

    Aligned ZnO nanorods were grown on ZnO/Si substrate via simple aqueous solution process at low-temperature of - 65 degrees C by using zinc nitrate and hexamethylenetetramine (HMTA). The detailed morphological and structural properties measured by FESEM, XRD, EDS and TEM confirmed that the as-grown nanorods are vertically aligned, well-crystalline possessing wurtzite hexagonal phase and grown along the [0001] direction. The room-temperature photoluminescence spectrum of the grown nanorods exhibited a strong and broad green emission and small ultraviolet emission. The as-prepared ZnO nanorods were post-annealed in nitrogen (N2) and oxygen (O2) environments and further characterized in terms of their morphological, structural and optical properties. After annealing the nanorods exhibit well-crystallinity and wurtzite hexagonal phase. Moreover, by annealing the PL spectra show the enhancement in the UV emission and suppression in the green emission. The presented results demonstrate that simply by post-annealing process, the optical properties of ZnO nanostructures can be controlled.

  4. 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.

  5. Ontological interpretation of biomedical database content.

    Science.gov (United States)

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

    2017-06-26

    addressed by a method that identifies implicit knowledge behind semantic annotations in biological databases and grounds it in an expressive upper-level ontology. The result is a seamless representation of database structure, content and annotations as OWL models.

  6. Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (economies. The main reason for this is the high deployment cost of FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment structure. Elastic

  7. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

    Science.gov (United States)

    Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

    2011-07-01

    The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

  8. Ontology Based Model Transformation Infrastructure

    NARCIS (Netherlands)

    Göknil, Arda; Topaloglu, N.Y.

    2005-01-01

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

  9. Ontology through a Mindfulness Process

    Science.gov (United States)

    Bearance, Deborah; Holmes, Kimberley

    2015-01-01

    Traditionally, when ontology is taught in a graduate studies course on social research, there is a tendency for this concept to be examined through the process of lectures and readings. Such an approach often leaves graduate students to grapple with a personal embodiment of this concept and to comprehend how ontology can ground their research.…

  10. 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

  11. L-GRAAL: Lagrangian graphlet-based network aligner.

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

    Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at

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

    Science.gov (United States)

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

    2012-09-21

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

  13. Remote sensing of local structure of the quasi-perpendicular Earth's bow shock by using field-aligned beams

    Directory of Open Access Journals (Sweden)

    B. Miao

    2009-03-01

    Full Text Available Field-aligned ion beams (FABs originate at the quasi-perpendicular Earth's bow shock and constitute an important ion population in the foreshock region. The bulk velocity of these FABs depends significantly on the shock normal angle, which is the angle between shock normal and upstream interplanetary magnetic field (IMF. This dependency may therefore be taken as an indicator of the local structure of the shock. Applying the direct reflection model to Cluster measurements, we have developed a method that uses proton FABs in the foreshock region for remote sensing of the local shock structure. The comparison of the model results with the multi-spacecraft observations of FAB events shows very good agreement in terms of wave amplitude and frequency of surface waves at the shock front.

  14. Band alignment in ZnSe/Zn1-x-yCdxMnySe quantum-well structures

    International Nuclear Information System (INIS)

    Yu, W.Y.; Salib, M.S.; Petrou, A.; Jonker, B.T.; Warnock, J.

    1997-01-01

    We present a magneto-optical study of ZnSe/Zn 1-x-y Cd x Mn y Se quantum-well structures in which a suitable choice of the Cd composition leads to a system that is type I at zero magnetic field. When a magnetic field is applied perpendicular to the layers of the structure, the band edges split in such a way as to make the upper σ - (1/2, t 3/2) exciton transition type II, while the ground state σ + (-1/2, -3/2) exciton component remains type I at all field values. This alignment reduces the probability for carrier relaxation from the higher-energy exciton component and opens the possibility of hole-spin population inversion via optical pumping. copyright 1997 The American Physical Society

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

    OpenAIRE

    Chuprina, Svetlana

    2016-01-01

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

  16. Synthesis, structure and magnetic properties of crystallographically aligned CuCr{sub 2}Se{sub 4} thin films

    Energy Technology Data Exchange (ETDEWEB)

    Esters, Marco [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Liebig, Andreas [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Ditto, Jeffrey J.; Falmbigl, Matthias [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Albrecht, Manfred [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Johnson, David C., E-mail: davej@uoregon.edu [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States)

    2016-06-25

    We report the low temperature synthesis of highly textured CuCr{sub 2}Se{sub 4} thin films using the modulated elemental reactant (MER) method. The structure of CuCr{sub 2}Se{sub 4} is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr{sub 2}Se{sub 4}. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the <111> axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr{sub 2}Se{sub 4} synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10{sup 6} erg cm{sup −3}; shape anisotropy: 1.07 × 10{sup 6} erg cm{sup −3}), with the easy axis lying out of plane, and a larger magnetic moment (6 μ{sub B}/f.u.) than bulk CuCr{sub 2}Se{sub 4}. - Highlights: • Crystallographically aligned, phase pure CuCr{sub 2}Se{sub 4} were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the <111> direction. • The magnetization is larger than bulk CuCr{sub 2}Se{sub 4} or other CuCr{sub 2}Se{sub 4} films made to date.

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

    Science.gov (United States)

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

    2016-10-04

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

  18. Business Ontology for Evaluating Corporate Social Responsibility

    OpenAIRE

    Ion Smeureanu; Andreea Dioşteanu; Camelia Delcea; Liviu Cotfas

    2011-01-01

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

  19. Precision alignment device

    Science.gov (United States)

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  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. A class of monolayer metal halogenides MX{sub 2}: Electronic structures and band alignments

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Feng; Wang, Weichao; Luo, Xiaoguang; Cheng, Yahui; Dong, Hong; Liu, Hui; Wang, Wei-Hua, E-mail: whwangnk@nankai.edu.cn [Department of Electronics and Tianjin Key Laboratory of Photo-Electronic Thin Film Device and Technology, Nankai University, Tianjin 300071 (China); Xie, Xinjian [School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130 (China)

    2016-03-28

    With systematic first principles calculations, a class of monolayer metal halogenides MX{sub 2} (M = Mg, Ca, Zn, Cd, Ge, Pb; M = Cl, Br, I) has been proposed. Our study indicates that these monolayer materials are semiconductors with the band gaps ranging from 2.03 eV of ZnI{sub 2} to 6.08 eV of MgCl{sub 2}. Overall, the band gap increases with the increase of the electronegativity of the X atom or the atomic number of the metal M. Meanwhile, the band gaps of monolayer MgX{sub 2} (X = Cl, Br) are direct while those of other monolayers are indirect. Based on the band edge curvatures, the derived electron (m{sub e}) and hole (m{sub h}) effective masses of MX{sub 2} monolayers are close to their corresponding bulk values except that the m{sub e} of CdI{sub 2} is three times larger and the m{sub h} for PbI{sub 2} is twice larger. Finally, the band alignments of all the studied MX{sub 2} monolayers are provided using the vacuum level as energy reference. These theoretical results may not only introduce the monolayer metal halogenides family MX{sub 2} into the emerging two-dimensional materials, but also provide insights into the applications of MX{sub 2} in future electronic, visible and ultraviolet optoelectronic devices.

  2. 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.

  3. Development of Ontology and 3D Software for the Diseases of Spine

    Directory of Open Access Journals (Sweden)

    Seungbock Lee

    2015-01-01

    Full Text Available KISTI is carrying out an e-Spine project for spinal diseases to prepare for the aged society, so-called NAP. The purpose of the study is to build a spine ontology that represents the anatomical structure and disease information which is compatible with simulation model of KISTI. The final use of the ontology includes diagnosis of diseases and setting treatment directions by the clinicians. The ontology was represented using 3D software. Twenty diseases were selected to be represented after discussions with a spine specialist. Several ontology studies were reviewed, reference books were selected for each disease and were organized in MS Excel. All the contents were then reviewed by the specialists. Altova SemanticWorks and Protégé were used to code spine ontology with OWL Full model. Links to the images from KISTI and sample images of diseases were included in the ontology. The OWL ontology was also reviewed by the specialists again with Protégé. We represented unidirectional ontology from anatomical structure to disease, images, and treatment. The ontology was human understandable. It would be useful for the education of medical students or residents studying diseases of spine. But in order for the computer to understand the ontology, a new model with OWL DL or Lite is needed.

  4. Science Fiction and Ontologies of Leadership

    Directory of Open Access Journals (Sweden)

    Jana Vizmuller-Zocco

    2014-12-01

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

  5. Logic and Ontology

    Directory of Open Access Journals (Sweden)

    Newton C. A. da Costa

    2002-12-01

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

  6. 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.

  7. 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.

  8. Relevance-based evaluation of alignment approaches: The OAEI2007 food task revisited

    NARCIS (Netherlands)

    Hage, W.R. van; Kolb, H.; Schreiber, G.

    2008-01-01

    Current state-of-the-art ontology-alignment evaluation methods are based on the assumption that alignment relations come in two flavors: correct and incorrect. Some alignment systems find more correct mappings than others and hence, by this assumption, they perform better. In practical applications

  9. Defining functional distances over Gene Ontology

    Directory of Open Access Journals (Sweden)

    del Pozo Angela

    2008-01-01

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

  10. Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

    Science.gov (United States)

    McKee, Rodney A.; Walker, Frederick J.

    2003-11-25

    A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

  11. Improved osteoblasts growth on osteomimetic hydroxyapatite/BaTiO_3 composites with aligned lamellar porous structure

    International Nuclear Information System (INIS)

    Liu, Beilei; Chen, Liangjian; Shao, Chunsheng; Zhang, Fuqiang; Zhou, Kechao; Cao, Jun; Zhang, Dou

    2016-01-01

    Osteoblasts growing into bone substitute is an important step of bone regeneration. This study prepared porous hydroxyapatite (HA)/BaTiO_3 piezoelectric composites with porosity of 40%, 50% and 60% by ice-templating method. Effects of HA/BaTiO_3 composites with different porosities, with and without polarizing treatment on adhesion, proliferation and differentiation of osteoblasts were investigated in vitro. Results revealed that cell densities of the porous groups were significantly higher than those of the dense group (p 0.05). The absence of mechanical loading on the polarized samples may account for this. The results indicated that hierarchically porous HA/BaTiO_3 played a favorable part in osteoblasts proliferation, differentiation and adhesion process and is a promising bone substitute material. - Graphical abstract: Aligned porous structure of HA/BaTiO_3 piezoelectric composites prepared by ice-templating method was similar to the lamellar Haversian system in bone tissue. When co-cultured with human osteosarcoma cells (MG63), porous HA/BaTiO_3 composites exhibited remarkable biological activity in promoting proliferation, differentiation and adhesion of MG63 cells. - Highlights: • The aligned porous structure of HA/BaTiO_3 composite was similar to the lamellar Haversian system in bone tissue. • The piezoelectric d_3_3 coefficient of HA/BaTiO_3 with porosity of 50% was 5.0 pC/N, much higher than that of natural bone. • HA/BaTiO_3 with porosity of 50% promoted proliferation, differentiation and adhesion of MG63 cells remarkably.

  12. Mould insert fabrication of a single-mode fibre connector alignment structure optimized by justified partial metallization

    International Nuclear Information System (INIS)

    Wissmann, Markus; Barié, Nicole; Guttmann, Markus; Schneider, Marc; Kolew, Alexander; Besser, Heino; Pfleging, Wilhelm; Hofmann, Andreas; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2015-01-01

    For mass production of multiscale-optical components, microstructured moulding tools are needed. Metal tools are used for hot embossing or injection moulding of microcomponents made of a thermoplastic polymer. Microstructures with extremely tight specifications, e.g. low side wall roughness and high aspect ratios are generally made by lithographic procedures such as x-ray lithography or deep proton writing. However, these processes are unsuitable for low-cost mass production. An alternative manufacturing method of moulding tools has been developed at the Karlsruhe Institute of Technology (KIT). This article describes a mould insert fabrication and a new replication process for self-centring fibre alignment structures for low loss field installable single-mode fibre connectors, developed and fabricated by the Vrije Universiteit Brussel (VUB) in collaboration with TE Connectivity. These components are to be used in fibre-to-the-home networks and support the deployment and maintenance of fibre optic links. The special feature of this particular fibre connector is a self-centring fibre alignment, achieved by means of a through hole with deflectable cantilevers acting as micro-springs. The particular challenge is the electroforming of through holes with a centre hole diameter smaller than 125 µm. The fibre connector structure is prototyped by deep proton writing in polymethylmethacrylate and used as a sacrificial part. Using joining, physical vapour deposition and electroforming technology, a negative copy of the prototyped connector is transferred into nickel to be used as a moulding tool. The benefits of this replication technique are a rapid and economical fabrication of moulding tools with high-precision microstructures and a long tool life. With these moulding tools low-cost mass production is possible. We present the manufacturing chain we have established. Each individual manufacturing step of the mould insert fabrication will be shown in this report. The

  13. Thermally Stable and Electrically Conductive, Vertically Aligned Carbon Nanotube/Silicon Infiltrated Composite Structures for High-Temperature Electrodes.

    Science.gov (United States)

    Zou, Qi Ming; Deng, Lei Min; Li, Da Wei; Zhou, Yun Shen; Golgir, Hossein Rabiee; Keramatnejad, Kamran; Fan, Li Sha; Jiang, Lan; Silvain, Jean-Francois; Lu, Yong Feng

    2017-10-25

    Traditional ceramic-based, high-temperature electrode materials (e.g., lanthanum chromate) are severely limited due to their conditional electrical conductivity and poor stability under harsh circumstances. Advanced composite structures based on vertically aligned carbon nanotubes (VACNTs) and high-temperature ceramics are expected to address this grand challenge, in which ceramic serves as a shielding layer protecting the VACNTs from the oxidation and erosive environment, while the VACNTs work as a conductor. However, it is still a great challenge to fabricate VACNT/ceramic composite structures due to the limited diffusion of ceramics inside the VACNT arrays. In this work, we report on the controllable fabrication of infiltrated (and noninfiltrated) VACNT/silicon composite structures via thermal chemical vapor deposition (CVD) [and laser-assisted CVD]. In laser-assisted CVD, low-crystalline silicon (Si) was quickly deposited at the VACNT subsurfaces/surfaces followed by the formation of high-crystalline Si layers, thus resulting in noninfiltrated composite structures. Unlike laser-assisted CVD, thermal CVD activated the precursors inside and outside the VACNTs simultaneously, which realized uniform infiltrated VACNT/Si composite structures. The growth mechanisms for infiltrated and noninfiltrated VACNT/ceramic composites, which we attributed to the different temperature distributions and gas diffusion mechanism in VACNTs, were investigated. More importantly, the as-farbicated composite structures exhibited excellent multifunctional properties, such as excellent antioxidative ability (up to 1100 °C), high thermal stability (up to 1400 °C), good high velocity hot gas erosion resistance, and good electrical conductivity (∼8.95 Sm -1 at 823 K). The work presented here brings a simple, new approach to the fabrication of advanced composite structures for hot electrode applications.

  14. There is no quantum ontology without classical ontology

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-07-01

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

  15. libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

    OpenAIRE

    Butt, Davin; Roger, Andrew J; Blouin, Christian

    2005-01-01

    Background An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used ...

  16. development of ontological knowledge representation

    African Journals Online (AJOL)

    Preferred Customer

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

  17. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

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

  18. Structural and photoluminescence characterization of vertically aligned multiwalled carbon nanotubes coated with ZnO by magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Ouldhamadouche, N. [Institut des Materiaux Jean Rouxel, Universite de Nantes, CNRS, 2 rue de la Houssiniere BP 32229 44322 Nantes cedex 3 (France); Laboratoire de Physique des Materiaux, Universite des Sciences et de la Technologie Houari Boumediene, BP 32 El Alla. 16111, Bab Ezzouaur (Algeria); Achour, A., E-mail: a_aminph@yahoo.fr [Institut des Materiaux Jean Rouxel, Universite de Nantes, CNRS, 2 rue de la Houssiniere BP 32229 44322 Nantes cedex 3 (France); Musa, I.; Ait Aissa, K.; Massuyeau, F.; Jouan, P.Y. [Institut des Materiaux Jean Rouxel, Universite de Nantes, CNRS, 2 rue de la Houssiniere BP 32229 44322 Nantes cedex 3 (France); Kechouane, M. [Laboratoire de Physique des Materiaux, Universite des Sciences et de la Technologie Houari Boumediene, BP 32 El Alla. 16111, Bab Ezzouaur (Algeria); Le Brizoual, L.; Faulques, E.; Barreau, N.; Djouadi, M.A. [Institut des Materiaux Jean Rouxel, Universite de Nantes, CNRS, 2 rue de la Houssiniere BP 32229 44322 Nantes cedex 3 (France)

    2012-05-01

    Zinc oxide (ZnO) nanostructures are very attractive in various optoelectronic applications such as light emitting devices. A fabrication process of these ZnO nanostructures which gives a good crystalline quality and being compatible with that of micro-fabrication has significant importance for practical application. In this work ZnO films with different thicknesses were deposited by RF-sputtering on vertically aligned multiwalled carbon nanotube (MWCNTs) template in order to obtain ZnO nanorods. The obtained hybrid structures (ZnO/MWCNTs) were characterized by scanning electron microscopy, X-ray diffraction, transmission electron microscopy, and time resolved photoluminescence spectroscopy (PL). Results show that the ZnO/MWCNTs have a nanorod structure like morphology with a good crystalline quality of the deposited ZnO on the MWCNTs. PL measurements reveal an enhancement of the band edge signal of ZnO/MWCNTs which is three times of magnitude higher compared to the ZnO film deposited on silicon. Moreover, the intensity enhancement varies as function of the ZnO thickness. Such hybrid structures are promising for optoelectronic application, such as blue-violet sources.

  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. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

    Directory of Open Access Journals (Sweden)

    Katja Seltmann

    2012-05-01

    Full Text Available Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arised from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, “preferred terms”, and “structural equivalency”. We also outline the use of Universal Resource Identifiers (URIs and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the “URI table” by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the “Analyzer” to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org. We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

  1. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr; Å kerman, Bjö rn; Nordé n, Bengt

    2012-01-01

    ) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong

  2. The shape-alignment relation in Lambda cold dark matter cosmic structures

    NARCIS (Netherlands)

    Basilakos, S; Plionis, M; Yepes, G; Gottlober, S; Turchaninov, [No Value

    2006-01-01

    In this paper, we study the supercluster-cluster morphological properties using one of the largest (2 x 512(3)) smoothed particle hydrodynamics (SPH)+N-body simulations of large-scale structure formation in a Lambda cold dark matter (Lambda CDM) model, based on the publicly available code GADGET. We

  3. Mediation, Alignment, and Information Services for Semantic interoperability (MAISSI): A Trade Study

    National Research Council Canada - National Science Library

    Barlos, Fotis; Hunter, Dan; Krikeles, Basil; McDonough, James

    2007-01-01

    .... Semantic Interoperability (SI) encompasses a broad range of technologies such as data mediation and schema matching, ontology alignment, and context representation that attempt to enable systems to understand each others semantics...

  4. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

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

    2018-06-01

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

  5. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

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

    2018-03-01

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

  6. Annotating the human genome with Disease Ontology

    Science.gov (United States)

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

    2009-01-01

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

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

    OpenAIRE

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

    1999-01-01

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

  8. A Strategy for Rapid Construction of Blood Vessel-Like Structures with Complex Cell Alignments.

    Science.gov (United States)

    Wang, Nuoxin; Peng, Yunhu; Zheng, Wenfu; Tang, Lixue; Cheng, Shiyu; Yang, Junchuan; Liu, Shaoqin; Zhang, Wei; Jiang, Xingyu

    2018-04-17

    A method is developed that can rapidly produce blood vessel-like structures by bonding cell-laden electrospinning (ES) films layer by layer using fibrin glue within 90 min. This strategy allows control of cell type, cell orientation, and material composition in separate layers. Furthermore, ES films with thicker fibers (polylactic-co-glycolic acid, fiber diameter: ≈3.7 µm) are used as cell-seeding layers to facilitate the cell in-growth; those with thinner fibers (polylactic acid, fiber diameter: ≈1.8 µm) are used as outer reinforcing layers to improve the mechanical strength and reduce the liquid leakage of the scaffold. Cells grow, proliferate, and migrate well in the multilayered structure. This design aims at a new type of blood vessel substitute with flexible control of parameters and implementation of functions. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. AlignMe—a membrane protein sequence alignment web server

    Science.gov (United States)

    Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

    2014-01-01

    We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

  10. ``Force,'' ontology, and language

    Science.gov (United States)

    Brookes, David T.; Etkina, Eugenia

    2009-06-01

    We introduce a linguistic framework through which one can interpret systematically students’ understanding of and reasoning about force and motion. Some researchers have suggested that students have robust misconceptions or alternative frameworks grounded in everyday experience. Others have pointed out the inconsistency of students’ responses and presented a phenomenological explanation for what is observed, namely, knowledge in pieces. We wish to present a view that builds on and unifies aspects of this prior research. Our argument is that many students’ difficulties with force and motion are primarily due to a combination of linguistic and ontological difficulties. It is possible that students are primarily engaged in trying to define and categorize the meaning of the term “force” as spoken about by physicists. We found that this process of negotiation of meaning is remarkably similar to that engaged in by physicists in history. In this paper we will describe a study of the historical record that reveals an analogous process of meaning negotiation, spanning multiple centuries. Using methods from cognitive linguistics and systemic functional grammar, we will present an analysis of the force and motion literature, focusing on prior studies with interview data. We will then discuss the implications of our findings for physics instruction.

  11. BIM – New rules of measurement ontology for construction cost estimation

    Directory of Open Access Journals (Sweden)

    F.H. Abanda

    2017-04-01

    Full Text Available For generations, the process of cost estimation has been manual, time-consuming and error-prone. Emerging Building Information Modelling (BIM can exploit standard measurement methods to automate cost estimation process and improve inaccuracies. Structuring standard measurement methods in an ontologically and machine readable format for a BIM software can greatly facilitate the process of improving inaccuracies in cost estimation. This study explores the development of an ontology based on New Rules of Measurement (NRM for cost estimation during the tendering stages. The methodology adopted is methontology, one of the most widely used ontology engineering methodologies. To ensure the ontology is fit for purpose, cost estimation experts are employed to check the semantics, descriptive logic-based reasoners are used to syntactically check the ontology and a leading 4D BIM modelling software is used on a case study building to test/validate the proposed ontology.

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

    Science.gov (United States)

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

    2015-09-22

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

  13. Exploring autophagy with Gene Ontology

    Science.gov (United States)

    2018-01-01

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

  14. Quick synthesis of highly aligned or randomly oriented nanofibrous structures composed of C60 molecules via self-assembly

    International Nuclear Information System (INIS)

    Kurosu, Shunji; Fukuda, Takahiro; Maekawa, Toru

    2013-01-01

    Assemblies, which are composed of nanoparticles such as nanofibres, have been intensively studied in recent years. This has particularly been the case in the field of biomedicine, where the aim is to develop efficient methodologies for capturing and separating target biomolecules and cells and/or encouraging bio-chemical reactions, utilizing the extremely high surface area to volume ratio of assemblies. There is an urgent need for the development of a quick synthesis method of forming nanofibrous structures on the surface of biomedical microchips and devices for the investigation of the interactions between biomolecules/cells and the nanostructures. Here, we produce nanofibrous structures composed of C 60 molecules, which are aligned in one direction or randomly oriented, by dissolving C 60 molecules and sulphur in benzene and evaporating a droplet of the solution on a glass substrate under appropriate conditions. The synthesis time is as short as 30 s. Sulphur is extracted and nanofibres are crystallized by leaving them in supercritical carbon dioxide. (paper)

  15. Structures and Correlations in Ideally Aligned Polar Gay-Berne Systems

    International Nuclear Information System (INIS)

    Longa, L.; Cholewiak, G.; Stelzer, J.

    2000-01-01

    We study an ideally oriented system of Gay-Berne particles with embedded longitudinal dipole moments. While keeping the translational degrees of freedom of the molecules unrestricted we assume that their dipoles can be oriented either parallel or antiparallel to the positive z axis of the laboratory frame. At high temperatures, this frustrated Gay-Berne mesogen exhibits an ideally oriented nematic phase, which is the reference state of the system. In the limit of vanishing dipole moment nematic, smectic-A and smectic B phases are stable. Interestingly, by changing the magnitude and location of the molecular dipole in the nematic reference state we found dipole-induced smectic A, smectic B and tetragonal crystal phases, in addition to crystalline structures with smectic A d and A 2 -like dipolar organization. Various singlet, pair and triplet distribution functions were evaluated to elucidate short and long range organization in these phases. In particular, the importance of triplet correlations for a proper understanding of the structures and their local, dipolar organization is demonstrated. (author)

  16. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    Science.gov (United States)

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

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

    Science.gov (United States)

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

    2014-12-08

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

  18. Improved osteoblasts growth on osteomimetic hydroxyapatite/BaTiO{sub 3} composites with aligned lamellar porous structure

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Beilei [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Chen, Liangjian, E-mail: jian007040@sina.com [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China); Shao, Chunsheng [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Zhang, Fuqiang; Zhou, Kechao [State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China); Cao, Jun [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Zhang, Dou, E-mail: dzhang@csu.edu.cn [State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China)

    2016-04-01

    Osteoblasts growing into bone substitute is an important step of bone regeneration. This study prepared porous hydroxyapatite (HA)/BaTiO{sub 3} piezoelectric composites with porosity of 40%, 50% and 60% by ice-templating method. Effects of HA/BaTiO{sub 3} composites with different porosities, with and without polarizing treatment on adhesion, proliferation and differentiation of osteoblasts were investigated in vitro. Results revealed that cell densities of the porous groups were significantly higher than those of the dense group (p < 0.05), so did the alkaline phosphate (ALP) and bone gla protein (BGP) activities. Porosity of 50% group exhibited higher ALP activity and BGP activity than those of the 40% and 60% groups. Scanning electron microscopy (SEM) observations revealed that osteoblasts adhered and stretched better on porous HA/BaTiO{sub 3} than on the dense one, especially HA/BaTiO{sub 3} with porosity of 50% and 60%. However, there was no significant difference in the cell morphology, cell densities, ALP and BGP activities between the polarized group and the non-polarized group (p > 0.05). The absence of mechanical loading on the polarized samples may account for this. The results indicated that hierarchically porous HA/BaTiO{sub 3} played a favorable part in osteoblasts proliferation, differentiation and adhesion process and is a promising bone substitute material. - Graphical abstract: Aligned porous structure of HA/BaTiO{sub 3} piezoelectric composites prepared by ice-templating method was similar to the lamellar Haversian system in bone tissue. When co-cultured with human osteosarcoma cells (MG63), porous HA/BaTiO{sub 3} composites exhibited remarkable biological activity in promoting proliferation, differentiation and adhesion of MG63 cells. - Highlights: • The aligned porous structure of HA/BaTiO{sub 3} composite was similar to the lamellar Haversian system in bone tissue. • The piezoelectric d{sub 33} coefficient of HA/BaTiO{sub 3} with porosity

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

    Science.gov (United States)

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

    2014-01-01

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

  20. Structural and electronic properties of Si/SiO2 MOS structures with aligned 3C-SiC nanocrystals in the oxide

    International Nuclear Information System (INIS)

    Pongracz, A.; Battistig, G.; Duecso, Cs.; Josepovits, K.V.; Deak, P.

    2007-01-01

    Our group previously proved that a simple reactive annealing in CO containing gas produces 3C-SiC nanocrystals, which are epitaxially and void-free aligned in the Si substrate. By a further thermal oxidation step, these nanocrystals can be lifted from the Si and incorporated into the SiO 2 matrix, thereby creating a promising structure for charge storage. In this work the structural and electrical properties of such systems with nanocrystalline SiC will be presented. Prototype MOS structures with 3C-SiC nanocrystals were produced for current-voltage and capacitance-voltage measurements. The results indicate that the high-temperature annealing did not damage the MOS structure, despite the fact that the CO annealing changed the electrical properties of the system. There was a positive charge accumulation and a reversible carrier injection observed in the structure. We assume that the positive charges originated from oxygen vacancies and the charge injection is related to the presence of SiC nanocrystals

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

    OpenAIRE

    Scharffe , François; Euzenat , Jérôme

    2011-01-01

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

  2. Use of the CIM Ontology

    Energy Technology Data Exchange (ETDEWEB)

    Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

    2006-02-08

    There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

  3. Minerals and aligned collagen fibrils in tilapia fish scales: structural analysis using dark-field and energy-filtered transmission electron microscopy and electron tomography.

    Science.gov (United States)

    Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki

    2011-10-01

    The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.

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

    DEFF Research Database (Denmark)

    Zambach, Sine; Madsen, Bodil Nistrup

    2009-01-01

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

  5. Supporting collaboration in interdisciplinary research of water–energy–food nexus by means of ontology engineering

    Directory of Open Access Journals (Sweden)

    Terukazu Kumazawa

    2017-06-01

    The introduction of ontology engineering approach will enable us to share a common language and a common theoretical basis. But the development of the new method based on ontology engineering is necessary. For example, knowledge structuring according to each perspective of researchers and simple figure accompanied with a reasoned argument in the background are the directions of tool development.

  6. 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 ...

  7. An extension of the Plant Ontology project supporting wood anatomy and development research

    NARCIS (Netherlands)

    Lens, F.; Cooper, L.; Gandolfo, M.A.; Groover, A.; Jaiswal, P.; Lachenbruch, B.; Spicer, R.; Staton, M.E.; Stevenson, D.W.; Walls, R.L.; Wegrzyn, J.

    2012-01-01

    The Wood Ontology project will provide a structured vocabulary and database resource that will be valuable for all scientists, including the IAWA community. To maximizethe utility of the resource and analyses it empowers, it is important for researchers to adopt the use of the ontology terms in the

  8. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    NARCIS (Netherlands)

    Kohler, S.; Doelken, S.C.; Mungall, C.J.; Bauer, S.; Firth, H.V.; Bailleul-Forestier, I.; Black, G.C.M.; Brown, D.L.; Brudno, M.; Campbell, J.; FitzPatrick, D.R.; Eppig, J.T.; Jackson, A.P.; Freson, K.; Girdea, M.; Helbig, I.; Hurst, J.A.; Jahn, J.; Jackson, L.G.; Kelly, A.M.; Ledbetter, D.H.; Mansour, S.; Martin, C.L.; Moss, C.; Mumford, A.; Ouwehand, W.H.; Park, S.M.; Riggs, E.R.; Scott, R.H.; Sisodiya, S.; Vooren, S. van der; Wapner, R.J.; Wilkie, A.O.; Wright, C.F.; Silfhout, A.T. van; Leeuw, N. de; Vries, B. de; Washingthon, N.L.; Smith, C.L.; Westerfield, M.; Schofield, P.; Ruef, B.J.; Gkoutos, G.V.; Haendel, M.; Smedley, D.; Lewis, S.E.; Robinson, P.N.

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have

  9. Protein complex prediction in large ontology attributed protein-protein interaction networks.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

    2013-01-01

    Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

  10. The influence of magnetic field on the cold neutral medium mass fraction and its alignment with density structures

    Science.gov (United States)

    Villagran, M. A.; Gazol, A.

    2018-06-01

    To contribute to the understanding of the magnetic field's influence on the segregation of cold neutral medium (CNM) in the solar neighbourhood we analyse magnetohydrodynamic simulations that include the main physical characteristics of the local neutral atomic interstellar medium. The simulations have a continuous solenoidal Fourier forcing in a periodic box of 100 pc per side and an initial uniform magnetic field (B_0) with intensities ranging between ˜0.4 and ˜8 μG. Our main results are as follows. (i) The CNM mass fraction diminishes with the increase in magnetic field intensity. (ii) There is a preferred alignment between CNM structures and B in all our B0 range but the preference weakens as B0 increases. It is worth noticing that this preference is also present in two-dimensional projections making an extreme angle (0 or π / 2) with respect to B_0 and it is only lost for the strongest magnetic field when the angle of projection is perpendicular to B_0. (iii) The aforementioned results are prevalent despite the inclusion of self-gravity in our continuously forced simulations with a mean density similar to the average value of the solar neighbourhood. (iv) Given a fixed B0 and slightly higher mean densities, up to double, the effects of self-gravity are still not qualitatively significant.

  11. New Three-Dimensional Porous Electrode Concept: Vertically-Aligned Carbon Nanotubes Directly Grown on Embroidered Copper Structures

    Directory of Open Access Journals (Sweden)

    Noemí Aguiló-Aguayo

    2017-12-01

    Full Text Available New three-dimensional (3D porous electrode concepts are required to overcome limitations in Li-ion batteries in terms of morphology (e.g., shapes, dimensions, mechanical stability (e.g., flexibility, high electroactive mass loadings, and electrochemical performance (e.g., low volumetric energy densities and rate capabilities. Here a new electrode concept is introduced based on the direct growth of vertically-aligned carbon nanotubes (VA-CNTs on embroidered Cu current collectors. The direct growth of VA-CNTs was achieved by plasma-enhanced chemical vapor deposition (PECVD, and there was no application of any post-treatment or cleaning procedure. The electrochemical behavior of the as-grown VA-CNTs was analyzed by charge/discharge cycles at different specific currents and with electrochemical impedance spectroscopy (EIS measurements. The results were compared with values found in the literature. The as-grown VA-CNTs exhibit higher specific capacities than graphite and pristine VA-CNTs found in the literature. This together with the possibilities that the Cu embroidered structures offer in terms of specific surface area, total surface area, and designs provide a breakthrough in new 3D electrode concepts.

  12. New Three-Dimensional Porous Electrode Concept: Vertically-Aligned Carbon Nanotubes Directly Grown on Embroidered Copper Structures.

    Science.gov (United States)

    Aguiló-Aguayo, Noemí; Amade, Roger; Hussain, Shahzad; Bertran, Enric; Bechtold, Thomas

    2017-12-11

    New three-dimensional (3D) porous electrode concepts are required to overcome limitations in Li-ion batteries in terms of morphology (e.g., shapes, dimensions), mechanical stability (e.g., flexibility, high electroactive mass loadings), and electrochemical performance (e.g., low volumetric energy densities and rate capabilities). Here a new electrode concept is introduced based on the direct growth of vertically-aligned carbon nanotubes (VA-CNTs) on embroidered Cu current collectors. The direct growth of VA-CNTs was achieved by plasma-enhanced chemical vapor deposition (PECVD), and there was no application of any post-treatment or cleaning procedure. The electrochemical behavior of the as-grown VA-CNTs was analyzed by charge/discharge cycles at different specific currents and with electrochemical impedance spectroscopy (EIS) measurements. The results were compared with values found in the literature. The as-grown VA-CNTs exhibit higher specific capacities than graphite and pristine VA-CNTs found in the literature. This together with the possibilities that the Cu embroidered structures offer in terms of specific surface area, total surface area, and designs provide a breakthrough in new 3D electrode concepts.

  13. High-Resolution Inkjet-Printed Oxide Thin-Film Transistors with a Self-Aligned Fine Channel Bank Structure.

    Science.gov (United States)

    Zhang, Qing; Shao, Shuangshuang; Chen, Zheng; Pecunia, Vincenzo; Xia, Kai; Zhao, Jianwen; Cui, Zheng

    2018-05-09

    A self-aligned inkjet printing process has been developed to construct small channel metal oxide (a-IGZO) thin-film transistors (TFTs) with independent bottom gates on transparent glass substrates. Poly(methylsilsesquioxane) was used to pattern hydrophobic banks on the transparent substrate instead of commonly used self-assembled octadecyltrichlorosilane. Photolithographic exposure from backside using bottom-gate electrodes as mask formed hydrophilic channel areas for the TFTs. IGZO ink was selectively deposited by an inkjet printer in the hydrophilic channel region and confined by the hydrophobic bank structure, resulting in the precise deposition of semiconductor layers just above the gate electrodes. Inkjet-printed IGZO TFTs with independent gate electrodes of 10 μm width have been demonstrated, avoiding completely printed channel beyond the broad of the gate electrodes. The TFTs showed on/off ratios of 10 8 , maximum mobility of 3.3 cm 2 V -1 s -1 , negligible hysteresis, and good uniformity. This method is conductive to minimizing the area of printed TFTs so as to the development of high-resolution printing displays.

  14. Field emission from a composite structure consisting of vertically aligned single-walled carbon nanotubes and carbon nanocones

    International Nuclear Information System (INIS)

    Yeh, C M; Chen, M Y; Hwang, J; Gan, J-Y; Kou, C S

    2006-01-01

    Vertically aligned single-walled carbon nanotubes (VA-SWCNTs) have been fabricated on carbon nanocones (CNCs) in a gravity-assisted chemical vapour deposition (CVD) process. The CNCs with nanoscale Co particles at the top were first grown on the Co/Si(100) substrate biased at 350 V in a plasma enhanced chemical vapour deposition process. The CNCs typically are ∼200 nm in height, and their diameters are ∼100 nm near the bottom and ∼10 nm at the top. The nanoscale Co particles ∼10 nm in diameter act as catalysts which favour the growth of VA-SWCNTs out of CNCs at 850 0 C in the gravity-assisted CVD process. The average length and the growth time of VA-SWCNTs are ∼150 nm and 1.5 min, equivalent to a growth rate of ∼6 μm h -1 . The diameters of VA-SWCNTs are estimated to be 1.2-2.1 nm. When VA-SWCNTs are fabricated on CNCs, the turn-on voltage is reduced from 3.9 to 0.7 V μm -1 and the emission current density at the electric field of 5 V μm -1 is enhanced by a factor of more than 200. The composite VA-SWCNT/CNC structure is potentially an excellent field emitter. The emission stability of the VA-SWCNT/CNC field emitter is discussed

  15. Toward semantic interoperability with linked foundational ontologies in ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-06-01

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

  16. Ontology construction and application in practice case study of health tourism in Thailand.

    Science.gov (United States)

    Chantrapornchai, Chantana; Choksuchat, Chidchanok

    2016-01-01

    Ontology is one of the key components in semantic webs. It contains the core knowledge for an effective search. However, building ontology requires the carefully-collected knowledge which is very domain-sensitive. In this work, we present the practice of ontology construction for a case study of health tourism in Thailand. The whole process follows the METHONTOLOGY approach, which consists of phases: information gathering, corpus study, ontology engineering, evaluation, publishing, and the application construction. Different sources of data such as structure web documents like HTML and other documents are acquired in the information gathering process. The tourism corpora from various tourism texts and standards are explored. The ontology is evaluated in two aspects: automatic reasoning using Pellet, and RacerPro, and the questionnaires, used to evaluate by experts of the domains: tourism domain experts and ontology experts. The ontology usability is demonstrated via the semantic web application and via example axioms. The developed ontology is actually the first health tourism ontology in Thailand with the published application.

  17. Complex Topographic Feature Ontology Patterns

    Science.gov (United States)

    Varanka, Dalia E.; Jerris, Thomas J.

    2015-01-01

    Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

  18. Geographic Ontologies, Gazetteers and Multilingualism

    Directory of Open Access Journals (Sweden)

    Robert Laurini

    2015-01-01

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

  19. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...

  20. Field-aligned structure of the storm time Pc 5 wave of November 14-15, 1979

    International Nuclear Information System (INIS)

    Takahashi, K.; Higbie, P.R.; Fennell, J.F.; Amata, E.

    1987-01-01

    Magnetic field data from the four satellites SCATHA (P78-2), GOES 2, GOES 3, and GEOS 2 have been analyzed to examine the magnetic field-aligned structure of a storm time Pc 5 wave that occurred on November 14-15, 1979. The wave had both transverse and compressional components. At a given instance the compressional and the radial components oscillated in phase of 180 degree out of phase, and the compressional and the azimuthal components oscillated +90 degree or -90 degree out of phase. In addition, each component changed its amplitude with magnetic latitude: the compressional component had a minimum at the magnetic equator, whereas the transverse components had a maximum at the equator and minima several degrees off the equator. A 180 degree relative phase switching among the components occurred across the latitudes of amplitude minima. From these observations the field line displacement of the wave is confirmed to have an antisymmetric standing structure about the magnetic equator with a parallel wave length of a few earth radii. The authors also observed other intriguing properties of the wave such as different parallel wave lengths of different field components and small-amplitude second harmonics near the nodes. A dielectric tensor appropriate for the ring current plasma is found to give an explanation for the relation between the polarization and the propagation of the wave. However, plasma data available from SCATHA does not support either the drift mirror instability of A. Hasegawa (1969) or the coupling between a drift mirror wave and a shear Alfven wave as discussed by A.D.M. Walker et al. (1982)

  1. 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...

  2. Addressing issues in foundational ontology mediation

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

  3. Technique for designing a domain ontology

    OpenAIRE

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

    2018-01-01

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

  4. 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

  5. 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...

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

    Science.gov (United States)

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

    2014-03-01

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

  7. Imitating intrinsic alignments: a bias to the CMB lensing-galaxy shape cross-correlation power spectrum induced by the large-scale structure bispectrum

    Science.gov (United States)

    Merkel, Philipp M.; Schäfer, Björn Malte

    2017-10-01

    Cross-correlating the lensing signals of galaxies and comic microwave background (CMB) fluctuations is expected to provide valuable cosmological information. In particular, it may help tighten constraints on parameters describing the properties of intrinsically aligned galaxies at high redshift. To access the information conveyed by the cross-correlation signal, its accurate theoretical description is required. We compute the bias to CMB lensing-galaxy shape cross-correlation measurements induced by non-linear structure growth. Using tree-level perturbation theory for the large-scale structure bispectrum, we find that the bias is negative on most angular scales, therefore mimicking the signal of intrinsic alignments. Combining Euclid-like galaxy lensing data with a CMB experiment comparable to the Planck satellite mission, the bias becomes significant only on smallest scales (ℓ ≳ 2500). For improved CMB observations, however, the corrections amount to 10-15 per cent of the CMB lensing-intrinsic alignment signal over a wide multipole range (10 ≲ ℓ ≲ 2000). Accordingly, the power spectrum bias, if uncorrected, translates into 2σ and 3σ errors in the determination of the intrinsic alignment amplitude in the case of CMB stage III and stage IV experiments, respectively.

  8. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

  9. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

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

  10. An Ontology for Knowledge Representation and Applications

    OpenAIRE

    Nhon Do

    2008-01-01

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

  11. ARMY CYBER STRUCTURE ALIGNMENT

    Science.gov (United States)

    2016-02-16

    content/?q=historic-cyber-unit-begins- daily-action . 14 John M. McHugh , Secretary of the Army, HQDA General Order 2014-02, Affirmation of Secretary of...support-plays-role-in-tactical-operations/75545442/. McHugh , John M., Secretary of the Army, HQDA General Order 2014-02, Affirmation of Secretary of

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

    Science.gov (United States)

    Tavva, Rajesh; Singh, Navjyoti

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

  13. Representations of spacetime: Formalism and ontological commitment

    Science.gov (United States)

    Bain, Jonathan Stanley

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

  14. An ontological approach to domain engineering

    NARCIS (Netherlands)

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

    2002-01-01

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

  15. Aspects of ontology visualization and integration

    NARCIS (Netherlands)

    Dmitrieva, Joelia Borisovna

    2011-01-01

    In this thesis we will describe and discuss methodologies for ontology visualization and integration. Two visualization methods will be elaborated. In one method the ontology is visualized with the node-link technique, and with the other method the ontology is visualized with the containment

  16. Derivation of Event-B Models from OWL Ontologies

    Directory of Open Access Journals (Sweden)

    Alkhammash Eman H.

    2016-01-01

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

  17. 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...

  18. Ontology and Appearing: Documentary Realism as a Mathematical Thought

    Directory of Open Access Journals (Sweden)

    Lindsey Hair

    2006-10-01

    Full Text Available This paper exposes the relation between the different mathematical orientations, on the one hand, and the modes of documentary film on the other. When we take, with Badiou, mathematics as ontology, and mathematical orientations as orientations to Being, we find in the structural similarity of mathematics and documentary an equivalence: between modes of documentaryand mathematical-ontological decisions, regarding the inscription of 'what is'. From here we move to consider Badiou's notion of 'in-appearing' through a reading of Alain Resnais' documentary Night and Fog.

  19. Facebook Ethnography: The Poststructural Ontology of Transnational (Im Migration Research

    Directory of Open Access Journals (Sweden)

    David Joseph Piacenti PhD

    2014-02-01

    Full Text Available This theoretical article discusses the creative utility of Facebook as a new ethnographic tool in which to study transnational (im migration. Facebook ethnography allows the (im migration researcher to transcend the four structural dualities that constrain transnational ethnographic research: (a geographic constraints, (b travel funding constraints, (c travel time constraints, and (d the logistical constraints of entrée into new ethnographic contexts. Facebook ethnography also allows the qualitative researcher to temporarily transcend the ontological structuralist dualities of traditional research methods, producing a new poststructural epistemological and ontological methodology.

  20. ODISEES: Ontology-Driven Interactive Search Environment for Earth Sciences

    Science.gov (United States)

    Rutherford, Matthew T.; Huffer, Elisabeth B.; Kusterer, John M.; Quam, Brandi M.

    2015-01-01

    This paper discusses the Ontology-driven Interactive Search Environment for Earth Sciences (ODISEES) project currently being developed to aid researchers attempting to find usable data among an overabundance of closely related data. ODISEES' ontological structure relies on a modular, adaptable concept modeling approach, which allows the domain to be modeled more or less as it is without worrying about terminology or external requirements. In the model, variables are individually assigned semantic content based on the characteristics of the measurements they represent, allowing intuitive discovery and comparison of data without requiring the user to sift through large numbers of data sets and variables to find the desired information.

  1. Aligned poly(L-lactic-co-e-caprolactone) electrospun microfibers and knitted structure: a novel composite scaffold for ligament tissue engineering.

    Science.gov (United States)

    Vaquette, Cédryck; Kahn, Cyril; Frochot, Céline; Nouvel, Cécile; Six, Jean-Luc; De Isla, Natalia; Luo, Li-Hua; Cooper-White, Justin; Rahouadj, Rachid; Wang, Xiong

    2010-09-15

    We developed a novel technique involving knitting and electrospinning to fabricate a composite scaffold for ligament tissue engineering. Knitted structures were coated with poly(L-lactic-co-e-caprolactone) (PLCL) and then placed onto a rotating cylinder and a PLCL solution was electrospun onto the structure. Highly aligned 2-microm-diameter microfibers covered the space between the stitches and adhered to the knitted scaffolds. The stress-strain tensile curves exhibited an initial toe region similar to the tensile behavior of ligaments. Composite scaffolds had an elastic modulus (150 +/- 14 MPa) similar to the modulus of human ligaments. Biological evaluation showed that cells proliferated on the composite scaffolds and they spontaneously orientated along the direction of microfiber alignment. The microfiber architecture also induced a high level of extracellular matrix secretion, which was characterized by immunostaining. We found that cells produced collagen type I and type III, two main components found in ligaments. After 14 days of culture, collagen type III started to form a fibrous network. We fabricated a composite scaffold having the mechanical properties of the knitted structure and the morphological properties of the aligned microfibers. It is difficult to seed a highly macroporous structure with cells, however the technique we developed enabled an easy cell seeding due to presence of the microfiber layer. Therefore, these scaffolds presented attractive properties for a future use in bioreactors for ligament tissue engineering. (c) 2010 Wiley Periodicals, Inc.

  2. Abnormal arrangement of a collagen/apatite extracellular matrix orthogonal to osteoblast alignment is constructed by a nanoscale periodic surface structure.

    Science.gov (United States)

    Matsugaki, Aira; Aramoto, Gento; Ninomiya, Takafumi; Sawada, Hiroshi; Hata, Satoshi; Nakano, Takayoshi

    2015-01-01

    Morphological and directional alteration of cells is essential for structurally appropriate construction of tissues and organs. In particular, osteoblast alignment is crucial for the realization of anisotropic bone tissue microstructure. In this article, the orientation of a collagen/apatite extracellular matrix (ECM) was established by controlling osteoblast alignment using a surface geometry with nanometer-sized periodicity induced by laser ablation. Laser irradiation induced self-organized periodic structures (laser-induced periodic surface structures; LIPSS) with a spatial period equal to the wavelength of the incident laser on the surface of biomedical alloys of Ti-6Al-4V and Co-Cr-Mo. Osteoblast orientation was successfully induced parallel to the grating structure. Notably, both the fibrous orientation of the secreted collagen matrix and the c-axis of the produced apatite crystals were orientated orthogonal to the cell direction. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy is controllable, including the characteristic organization of a collagen/apatite composite orthogonal to the osteoblast orientation, by controlling the cell alignment using periodic surface geometry. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    KAUST Repository

    Hoehndorf, Robert

    2016-11-14

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

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

    Science.gov (United States)

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

    2016-11-14

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

  5. 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

  6. Emotion Education without Ontological Commitment?

    Science.gov (United States)

    Kristjansson, Kristjan

    2010-01-01

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

  7. Ontological problems of contemporary linguistics

    Directory of Open Access Journals (Sweden)

    А В Бондаренко

    2009-03-01

    Full Text Available The article studies linguistic ontology problems such as evolution of essential-existential views of language, interrelation within Being-Language-Man triad, linguistics gnosiological principles, language essence localization, and «expression» as language metalinguistic unit as well as architectonics of language personality et alia.

  8. An ontological approach to logistics

    NARCIS (Netherlands)

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

    2013-01-01

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

  9. A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies

    Science.gov (United States)

    Ochs, Christopher; Geller, James; Perl, Yehoshua; Musen, Mark A.

    2016-01-01

    Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving “live partial-area taxonomies” is demonstrated. PMID:27345947

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

    Science.gov (United States)

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

    2017-11-09

    model for druggable targets including various related information such as protein, gene, protein domain, protein structure, binding site, small molecule drug, mechanism of action, protein tissue localization, disease association, and many other types of information. DTO will further facilitate the otherwise challenging integration and formal linking to biological assays, phenotypes, disease models, drug poly-pharmacology, binding kinetics and many other processes, functions and qualities that are at the core of drug discovery. The first version of DTO is publically available via the website http://drugtargetontology.org/ , Github ( http://github.com/DrugTargetOntology/DTO ), and the NCBO Bioportal ( http://bioportal.bioontology.org/ontologies/DTO ). The long-term goal of DTO is to provide such an integrative framework and to populate the ontology with this information as a community resource.

  11. 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.

  12. A novel design of hidden web crawler using ontology

    OpenAIRE

    Manvi; Bhatia, Komal Kumar; Dixit, Ashutosh

    2015-01-01

    Deep Web is content hidden behind HTML forms. Since it represents a large portion of the structured, unstructured and dynamic data on the Web, accessing Deep-Web content has been a long challenge for the database community. This paper describes a crawler for accessing Deep-Web using Ontologies. Performance evaluation of the proposed work showed that this new approach has promising results.

  13. Self-Assembly of Chip-Size Components with Cavity Structures: High-Precision Alignment and Direct Bonding without Thermal Compression for Hetero Integration

    Directory of Open Access Journals (Sweden)

    Mitsumasa Koyanagi

    2011-02-01

    Full Text Available New surface mounting and packaging technologies, using self-assembly with chips having cavity structures, were investigated for three-dimensional (3D and hetero integration of complementary metal-oxide semiconductors (CMOS and microelectromechanical systems (MEMS. By the surface tension of small droplets of 0.5 wt% hydrogen fluoride (HF aqueous solution, the cavity chips, with a side length of 3 mm, were precisely aligned to hydrophilic bonding regions on the surface of plateaus formed on Si substrates. The plateaus have micro-channels to readily evaporate and fully remove the liquid from the cavities. The average alignment accuracy of the chips with a 1 mm square cavity was found to be 0.4 mm. The alignment accuracy depends, not only on the area of the bonding regions on the substrates and the length of chip periphery without the widths of channels in the plateaus, but also the area wetted by the liquid on the bonding regions. The precisely aligned chips were then directly bonded to the substrates at room temperature without thermal compression, resulting in a high shear bonding strength of more than 10 MPa.

  14. Gradient Learning Algorithms for Ontology Computing

    Science.gov (United States)

    Gao, Wei; Zhu, Linli

    2014-01-01

    The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting. PMID:25530752

  15. Gradient Learning Algorithms for Ontology Computing

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2014-01-01

    Full Text Available The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting.

  16. History Matters: Incremental Ontology Reasoning Using Modules

    Science.gov (United States)

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

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

  17. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  19. Growth and field emission properties of one-dimensional carbon composite structure consisting of vertically aligned carbon nanotubes and nanocones

    International Nuclear Information System (INIS)

    Zhang Hongxin; Feng, Peter X; Fonseca, Luis; Morell, Gerardo; Makarov, Vladimir I; Weiner, Brad R

    2009-01-01

    A simple approach is demonstrated for quickly growing a large-area aligned carbon composite nanostructure consisting of vertically aligned nanotubes and nanocones by the catalyst-assisted pulsed laser deposition techniques. The pyrolytic graphite was used as carbon source. The carbon nanocones were first grown on the molybdenum substrate with Ni catalysts. The carbon nanotubes have a uniform shape and length, aligned vertically on carbon nanocones, and the average diameter is about 7 nm. The special carbon composite arrays exhibit excellent field emission behaviours. The long-term field emission current stability of the one-dimensioned carbon nanostructure has also been investigated. No obvious current density decay was observed after a 10-day continuous experiment, indicating the super stability of the sample as cathode material.

  20. Learning of Alignment Rules between Concept Hierarchies

    Science.gov (United States)

    Ichise, Ryutaro; Takeda, Hideaki; Honiden, Shinichi

    With the rapid advances of information technology, we are acquiring much information than ever before. As a result, we need tools for organizing this data. Concept hierarchies such as ontologies and information categorizations are powerful and convenient methods for accomplishing this goal, which have gained wide spread acceptance. Although each concept hierarchy is useful, it is difficult to employ multiple concept hierarchies at the same time because it is hard to align their conceptual structures. This paper proposes a rule learning method that inputs information from a source concept hierarchy and finds suitable location for them in a target hierarchy. The key idea is to find the most similar categories in each hierarchy, where similarity is measured by the κ(kappa) statistic that counts instances belonging to both categories. In order to evaluate our method, we conducted experiments using two internet directories: Yahoo! and LYCOS. We map information instances from the source directory into the target directory, and show that our learned rules agree with a human-generated assignment 76% of the time.

  1. Band alignment studies of Al2O3/CuGaO2 and ZnO/CuGaO2 hetero-structures grown by pulsed laser deposition

    International Nuclear Information System (INIS)

    Ajimsha, R.S.; Das, Amit K.; Joshi, M.P.; Kukreja, L.M.

    2014-01-01

    Highlights: • Band offset studies at the interface of Al 2 O 3 /CuGaO 2 and ZnO/CuGaO 2 hetero-structures were performed using X-ray photoelectron spectroscopy. • Valance band offsets (VBO) of these hetero-structures were obtained from respective XPS peak positions and VB spectra using Kraut's equation. • Al 2 O 3 /CuGaO 2 interface exhibited a type I band alignment with valance band offset (VBO) of 4.05 eV whereas type II band alignment was observed in ZnO/CuGaO 2 hetero-structure with a VBO of 2.32 eV. • Schematic band alignment diagram for the interface of these hetero-structures has been constructed. • Band offset and alignment studies of these heterojunctions are important for gaining insight to the design of various optoelectronic devices based on such hetero-structures. - Abstract: We have studied the band offset and alignment of pulsed laser deposited Al 2 O 3 /CuGaO 2 and ZnO/CuGaO 2 hetero-structures using photoelectron spectroscopy. Al 2 O 3 /CuGaO 2 interface exhibited a type I band alignment with valance band offset (VBO) of 4.05 eV whereas type II band alignment was observed in ZnO/CuGaO 2 hetero-structure with a VBO of 2.32 eV. Schematic band alignment diagram for the interface of these hetero-structures has been constructed. Band offset and alignment studies of these heterojunctions are important for gaining insight to the design of various optoelectronic devices based on such hetero-structures

  2. 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.

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

    CERN Document Server

    Munir, Kamran; Bloodsworth, Peter; McClatchey, Richard

    2008-01-01

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

  4. Structure of the auroral precipitation region in the dawn sector: relationship to convection reversal boundaries and field-aligned currents

    Directory of Open Access Journals (Sweden)

    Y. I. Feldstein

    2001-05-01

    precipitation (AO is mapped to the dawn periphery of the Central Plasma Sheet (CPS; the soft small scale structured precipitation (SSSL is mapped to the outer magnetosphere close to the magnetopause, i.e. the Low Latitude Boundary Layer (LLBL. In the near-noon sector, earthward fluxes of soft electrons, which cause the Diffuse Red Aurora (DRA, are observed. The ion energies decrease with increasing latitude. The plasma spectra of the DRA regime are analogous to the spectra of the Plasma Mantle (PM. In the dawn sector, the large-scale field-aligned currents flow into the ionosphere at the SSSL latitudes (Region 1 and flow out at the AO or DAZ latitudes (Region 2. In the dawn and dusk sectors, the large-scale Region 1 and Region 2 FAC generation occurs in different plasma domains of the distant magnetosphere. The dawn and dusk FAC connection to the traditional Region 1 and Region 2 has only formal character, as FAC generating in various magnetospheric plasma domains integrate in the same region (Region 1 or Region 2. In the SSSL, there is anti-sunward convection; in the DAZ and the AO, there is the sunward convection. At PM latitudes, the convection is controlled by the azimuthal IMF component (By . It is suggested to extend the notation of the plasma pattern boundaries, as proposed by Newell et al. (1996, for the nightside sector of the auroral oval to the dawn sector.Key words. Magnetospheric physics (current systems; magnetospheric configuration and dynamics; plasma convection

  5. Structure of the auroral precipitation region in the dawn sector: relationship to convection reversal boundaries and field-aligned currents

    Directory of Open Access Journals (Sweden)

    Y. I. Feldstein

    electrons and isotropic ion precipitation (AO is mapped to the dawn periphery of the Central Plasma Sheet (CPS; the soft small scale structured precipitation (SSSL is mapped to the outer magnetosphere close to the magnetopause, i.e. the Low Latitude Boundary Layer (LLBL. In the near-noon sector, earthward fluxes of soft electrons, which cause the Diffuse Red Aurora (DRA, are observed. The ion energies decrease with increasing latitude. The plasma spectra of the DRA regime are analogous to the spectra of the Plasma Mantle (PM. In the dawn sector, the large-scale field-aligned currents flow into the ionosphere at the SSSL latitudes (Region 1 and flow out at the AO or DAZ latitudes (Region 2. In the dawn and dusk sectors, the large-scale Region 1 and Region 2 FAC generation occurs in different plasma domains of the distant magnetosphere. The dawn and dusk FAC connection to the traditional Region 1 and Region 2 has only formal character, as FAC generating in various magnetospheric plasma domains integrate in the same region (Region 1 or Region 2. In the SSSL, there is anti-sunward convection; in the DAZ and the AO, there is the sunward convection. At PM latitudes, the convection is controlled by the azimuthal IMF component (By . It is suggested to extend the notation of the plasma pattern boundaries, as proposed by Newell et al. (1996, for the nightside sector of the auroral oval to the dawn sector.

    Key words. Magnetospheric physics (current systems; magnetospheric configuration and dynamics; plasma convection

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

    Science.gov (United States)

    Smith, Barry; Ceusters, Werner

    2010-11-15

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

  7. RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

    Czech Academy of Sciences Publication Activity Database

    Widmann, J.; Stombaugh, J.; McDonald, D.; Chocholoušová, Jana; Gardner, P.; Iyer, M.; Liu, Z.; Lozupone, C. A.; Quinn, J.; Smit, S.; Wikman, S.; Zaneveld, J. R. R.; Knight, R.

    2012-01-01

    Roč. 18, č. 7 (2012), s. 1319-1327 ISSN 1355-8382 R&D Projects: GA MŠk ME09019 Institutional research plan: CEZ:AV0Z40550506 Keywords : RNA * RNASTAR * alignment * repository Subject RIV: CC - Organic Chemistry Impact factor: 5.088, year: 2012

  8. Low-Energy Dislocation Structure (LEDS) character of dislocation boundaries aligned with slip planes in rolled aluminium

    DEFF Research Database (Denmark)

    Winther, Grethe; Hong, Chuanshi; Huang, Xiaoxu

    2015-01-01

    For the specific slip geometry of two sets of coplanar systems (a total of four systems) in fcc metals, the range of dislocation networks in boundaries aligned with one of the two active slip planes is predicted from the Frank equation for boundaries free of long-range elastic stresses. Detailed...

  9. Structural, electronic structure, and band alignment properties at epitaxial NiO/Al{sub 2}O{sub 3} heterojunction evaluated from synchrotron based X-ray techniques

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S. D., E-mail: devsh@rrcat.gov.in; Das, Arijeet; Ajimsha, R. S.; Upadhyay, Anuj; Kamparath, Rajiv; Mukherjee, C.; Misra, P.; Rai, S. K.; Sinha, A. K.; Ganguli, Tapas [Raja Ramanna Centre for Advanced Technology, Indore, Madhya Pradesh 452013 (India); Nand, Mangla; Jha, S. N. [Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085 (India); Shukla, D. K.; Phase, D. M. [UGC-DAE Consortium for Scientific Research, Khandwa Road, Indore, Madhya Pradesh 452017 (India)

    2016-04-28

    The valence band offset value of 2.3 ± 0.2 eV at epitaxial NiO/Al{sub 2}O{sub 3} heterojunction is determined from photoelectron spectroscopy experiments. Pulsed laser deposited thin film of NiO on Al{sub 2}O{sub 3} substrate is epitaxially grown along [111] direction with two domain structures, which are in-plane rotated by 60° with respect to each other. Observation of Pendellosung oscillations around Bragg peak confirms high interfacial and crystalline quality of NiO layer deposited on Al{sub 2}O{sub 3} substrate. Surface related feature in Ni 2p{sub 3/2} core level spectra along with oxygen K-edge soft X-ray absorption spectroscopy results indicates that the initial growth of NiO on Al{sub 2}O{sub 3} substrate is in the form of islands, which merge to form NiO layer for the larger coverage. The value of conduction band offset is also evaluated from the measured values of band gaps of NiO and Al{sub 2}O{sub 3} layers. A type-I band alignment at NiO and Al{sub 2}O{sub 3} heterojunction is also obtained. The determined values of band offsets can be useful in heterojunction based light emitting devices.

  10. Multicriteria analysis of ontologically represented information

    Science.gov (United States)

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

    2014-11-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  12. 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.

  13. Ontology Matching Across Domains

    Science.gov (United States)

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  14. Formal Ontologies and Uncertainty. In Geographical Knowledge

    Directory of Open Access Journals (Sweden)

    Matteo Caglioni

    2014-05-01

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

  15. Nova laser alignment control system

    International Nuclear Information System (INIS)

    Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

    1984-01-01

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system

  16. The Christological Ontology of Reason

    DEFF Research Database (Denmark)

    Nissen, Ulrik Becker

    2006-01-01

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

  17. Emotion Ontology for Context Awareness

    OpenAIRE

    Berthelon , Franck; Sander , Peter

    2013-01-01

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

  18. Towards an Ontology of Software

    OpenAIRE

    Wang, Xiaowei

    2016-01-01

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

  19. 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.

  20. MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

    Science.gov (United States)

    Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

    2013-11-25

    We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

  1. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

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

    Directory of Open Access Journals (Sweden)

    Hakenberg Jörg

    2009-01-01

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

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

    Science.gov (United States)

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

    2012-01-06

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

  4. Self-organizing ontology of biochemically relevant small molecules

    Science.gov (United States)

    2012-01-01

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

  5. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

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

  6. Alignment of whole genomes.

    Science.gov (United States)

    Delcher, A L; Kasif, S; Fleischmann, R D; Peterson, J; White, O; Salzberg, S L

    1999-01-01

    A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications. PMID:10325427

  7. Ultrasonic welding for fast bonding of self-aligned structures in lab-on-a-chip systems

    DEFF Research Database (Denmark)

    Kistrup, Kasper; Poulsen, Carl Esben; Hansen, Mikkel Fougt

    2015-01-01

    Ultrasonic welding is a rapid, promising bonding method for the bonding of polymer chips; yet its use is still limited. We present two lab-on-a-chip applications where ultrasonic welding can be preferably applied: (1) Self-aligned gapless bonding of a two-part chip with a tolerance of 50 um; (2...... solutions offered here can significantly help bridge the gap between academia and industry, where the differences in production methods and materials pose a challenge when transferring technology....

  8. Development and Evaluation of an Obesity Ontology for Social Big Data Analysis.

    Science.gov (United States)

    Kim, Ae Ran; Park, Hyeoun-Ae; Song, Tae-Min

    2017-07-01

    The aim of this study was to develop and evaluate an obesity ontology as a framework for collecting and analyzing unstructured obesity-related social media posts. The obesity ontology was developed according to the 'Ontology Development 101'. The coverage rate of the developed ontology was examined by mapping concepts and terms of the ontology with concepts and terms extracted from obesity-related Twitter postings. The structure and representative ability of the ontology was evaluated by nurse experts. We applied the ontology to the density analysis of keywords related to obesity types and management strategies and to the sentiment analysis of obesity and diet using social big data. The developed obesity ontology was represented by 8 superclasses and 124 subordinate classes. The superclasses comprised 'risk factors,' 'types,' 'symptoms,' 'complications,' 'assessment,' 'diagnosis,' 'management strategies,' and 'settings.' The coverage rate of the ontology was 100% for the concepts and 87.8% for the terms. The evaluation scores for representative ability were higher than 4.0 out of 5.0 for all of the evaluation items. The density analysis of keywords revealed that the top-two posted types of obesity were abdomen and thigh, and the top-three posted management strategies were diet, exercise, and dietary supplements or drug therapy. Positive expressions of obesity-related postings has increased annually in the sentiment analysis. It was found that the developed obesity ontology was useful to identify the most frequently used terms on obesity and opinions and emotions toward obesity posted by the geneal population on social media.

  9. 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.

  10. Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

    Science.gov (United States)

    Lovering, Ruth C; Roncaglia, Paola; Howe, Douglas G; Laulederkind, Stanley J F; Khodiyar, Varsha K; Berardini, Tanya Z; Tweedie, Susan; Foulger, Rebecca E; Osumi-Sutherland, David; Campbell, Nancy H; Huntley, Rachael P; Talmud, Philippa J; Blake, Judith A; Breckenridge, Ross; Riley, Paul R; Lambiase, Pier D; Elliott, Perry M; Clapp, Lucie; Tinker, Andrew; Hill, David P

    2018-02-01

    A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects. © 2018 The Authors.

  11. OAHG: an integrated resource for annotating human genes with multi-level ontologies.

    Science.gov (United States)

    Cheng, Liang; Sun, Jie; Xu, Wanying; Dong, Lixiang; Hu, Yang; Zhou, Meng

    2016-10-05

    OAHG, an integrated resource, aims to establish a comprehensive functional annotation resource for human protein-coding genes (PCGs), miRNAs, and lncRNAs by multi-level ontologies involving Gene Ontology (GO), Disease Ontology (DO), and Human Phenotype Ontology (HPO). Many previous studies have focused on inferring putative properties and biological functions of PCGs and non-coding RNA genes from different perspectives. During the past several decades, a few of databases have been designed to annotate the functions of PCGs, miRNAs, and lncRNAs, respectively. A part of functional descriptions in these databases were mapped to standardize terminologies, such as GO, which could be helpful to do further analysis. Despite these developments, there is no comprehensive resource recording the function of these three important types of genes. The current version of OAHG, release 1.0 (Jun 2016), integrates three ontologies involving GO, DO, and HPO, six gene functional databases and two interaction databases. Currently, OAHG contains 1,434,694 entries involving 16,929 PCGs, 637 miRNAs, 193 lncRNAs, and 24,894 terms of ontologies. During the performance evaluation, OAHG shows the consistencies with existing gene interactions and the structure of ontology. For example, terms with more similar structure could be associated with more associated genes (Pearson correlation γ 2  = 0.2428, p < 2.2e-16).

  12. An Ontological Architecture for Orbital Debris Data

    OpenAIRE

    Rovetto, Robert J.

    2017-01-01

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

  13. Versioning System for Distributed Ontology Development

    Science.gov (United States)

    2016-03-15

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

  14. A variational image-based approach to the correction of susceptibility artifacts in the alignment of diffusion weighted and structural MRI.

    Science.gov (United States)

    Tao, Ran; Fletcher, P Thomas; Gerber, Samuel; Whitaker, Ross T

    2009-01-01

    This paper presents a method for correcting the geometric and greyscale distortions in diffusion-weighted MRI that result from inhomogeneities in the static magnetic field. These inhomogeneities may due to imperfections in the magnet or to spatial variations in the magnetic susceptibility of the object being imaged--so called susceptibility artifacts. Echo-planar imaging (EPI), used in virtually all diffusion weighted acquisition protocols, assumes a homogeneous static field, which generally does not hold for head MRI. The resulting distortions are significant, sometimes more than ten millimeters. These artifacts impede accurate alignment of diffusion images with structural MRI, and are generally considered an obstacle to the joint analysis of connectivity and structure in head MRI. In principle, susceptibility artifacts can be corrected by acquiring (and applying) a field map. However, as shown in the literature and demonstrated in this paper, field map corrections of susceptibility artifacts are not entirely accurate and reliable, and thus field maps do not produce reliable alignment of EPIs with corresponding structural images. This paper presents a new, image-based method for correcting susceptibility artifacts. The method relies on a variational formulation of the match between an EPI baseline image and a corresponding T2-weighted structural image but also specifically accounts for the physics of susceptibility artifacts. We derive a set of partial differential equations associated with the optimization, describe the numerical methods for solving these equations, and present results that demonstrate the effectiveness of the proposed method compared with field-map correction.

  15. 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

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

    DEFF Research Database (Denmark)

    Seibt, Johanna

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

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

    OpenAIRE

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

    2007-01-01

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

  18. The NASA Air Traffic Management Ontology (atmonto)

    Data.gov (United States)

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

  19. Ontology Enabled Generation of Embedded Web Services

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  20. Scientific Digital Libraries, Interoperability, and Ontologies

    Science.gov (United States)

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

    2009-01-01

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

  1. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

    Fabritius, Christina; Madsen, Nadia; Clausen, Jens

    2006-01-01

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

  2. Finding the best visualization of an ontology

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  3. The current landscape of pitfalls in Ontologies

    CSIR Research Space (South Africa)

    Keet, CM

    2013-09-01

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

  4. DEPONTO: A Reusable Dependability Domain Ontology

    Directory of Open Access Journals (Sweden)

    Teodora Sanislav

    2015-08-01

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

  5. Ontological Engineering for the Cadastral Domain

    DEFF Research Database (Denmark)

    Stubkjær, Erik; Stuckenschmidt, Heiner

    2000-01-01

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

  6. Vaccine and Drug Ontology Studies (VDOS 2014).

    Science.gov (United States)

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2016-01-01

    The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies.

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

    Directory of Open Access Journals (Sweden)

    Skene JH Pate

    2007-09-01

    Full Text Available Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD, which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1 install Apache Tomcat 2 on one's web server, (2 download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3 create an html (HyperText Markup Language file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed Ontology

  8. Ontology for customer centric digital services and analytics

    Science.gov (United States)

    Keat, Ng Wai; Shahrir, Mohammad Shazri

    2017-11-01

    In computer science research, ontologies are commonly utilised to create a unified abstract across many rich and different fields. In this paper, we apply the concept to the customer centric domain of digital services analytics and present an analytics solution ontology. The essence is based from traditional Entity Relationship Diagram (ERD), which then was abstracted out to cover wider areas on customer centric digital services. The ontology we developed covers both static aspects (customer identifiers) and dynamic aspects (customer's temporal interactions). The structure of the customer scape is modeled with classes that represent different types of customer touch points, ranging from digital and digital-stamps which represent physical analogies. The dynamic aspects of customer centric digital service are modeled with a set of classes, with the importance is represented in different associations involving establishment and termination of the target interaction. The realized ontology can be used in development of frameworks for customer centric applications, and for specification of common data format used by cooperating digital service applications.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-01-04

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

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

    Science.gov (United States)

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

    2013-05-01

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

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

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F.

    2011-01-01

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

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

    Science.gov (United States)

    Bachore, Zelalem

    2012-01-01

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

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

    Science.gov (United States)

    Soares, Andrey

    2009-01-01

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

  18. The Quest to Solve Problems That Don’t Exist: Thought Artifacts in Contemporary Ontology

    Directory of Open Access Journals (Sweden)

    Kastrup Bernardo

    2017-10-01

    Full Text Available Questions about the nature of reality and consciousness remain unresolved in philosophy today, but not for lack of hypotheses. Ontologies as varied as physicalism, microexperientialism and cosmopsychism enrich the philosophical menu. Each of these ontologies faces a seemingly fundamental problem: under physicalism, for instance, we have the ‘hard problem of consciousness,’ whereas under microexperientialism we have the ‘subject combination problem.’ I argue that these problems are thought artifacts, having no grounding in empirical reality. In a manner akin to semantic paradoxes, they exist only in the internal logico-conceptual structure of their respective ontologies.

  19. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

    Science.gov (United States)

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

    2017-06-07

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

  20. Extraction d'association d'EIM à partir de dossiers patients : expérimentation avec les structures de patrons et les ontologies

    OpenAIRE

    Personeni , Gabin; Devignes , Marie-Dominique; Dumontier , Michel; Smaïl-Tabbone , Malika; Coulet , Adrien

    2016-01-01

    National audience; Les Dossiers Médicaux Electroniques (DME) constituent une ressource de grand intérêt pour étudier les Evènements Indésirables Médicamenteux (EIM). Nous proposons ici de fouiller les DME pour identifier des EIM fréquemment associés dans des sous-groupes de patients. Les EIM ayant des manifestations complexes, nous utilisons l'analyse formelle de concepts et ses structures de patrons, un cadre mathématique permettant la généralisation, en exploitant les connaissances du domai...

  1. Motions of CMS Detector structures due to the magnetic field forces as observed by the Link Alignment System during the Test of the 4 Tesla Magnet Solenoid

    CERN Document Server

    Calderón, Alicia; González-Sánchez, F J; Martínez-Rivero, C; Matorras, Francisco; Rodrigo, Teresa; Martínez, P; Scodellaro, Luca; Sobrón, M; Vila, Ivan; Virto, A L; Alberdi, Javier; Arce, Pedro; Barcala, Jose Miguel; Calvo, Enrique; Ferrando, Antonio; Josa-Mutuberria, I; Molinero, Antonio; Navarrete, Jose Javier; Oller, Juan Carlos; Yuste, Ceferino

    2008-01-01

    This document describes results obtained from the Link Alignment System data recorded during the CMS Magnet Test. A brief description of the system is followed by the discussion of the detected relative displacements (from micrometres to centimetres) between detector elements and rotations of detector structures (from microradians to milliradians). Observed displacements are studied as functions of the magnetic field intensity. In addition, the reconstructed positions of active element sensors are compared to their positions as measured by photogrammetry and the reconstructed motions due to the magnetic field strength are described.

  2. Motions of CMS Detector Structures as Observed by the Link Alignment System during the Test of the 4 Tesla Magnet Solenoid

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J.; Arce, P.; Barcala, J. M.; Calvo, E.; Ferramdp, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.; Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martin-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Scodellaro, L.; Sobron, M.; Vila, I.; Virto, A. L.

    2008-07-01

    This document describes results obtained from the Link Alignment System data recorded during the CMS Magnet Test. A brief description of the system is followed by the discussion of the detected relative displacements (from micro metres to centimetres) between detector elements and rotation of detector structures (from microradiants to milliradiants). Observed displacements are studied as functions of the magnetic fi eld intensity. In addition, a comparison of the reconstructed position of active element sensors with respect to their position as measured by photogrammetry is made and the reconstructed motions due to the magnetic field strength are described. (Author) 19 refs.

  3. The CMS Experiment: on and under Ground Motions of Structures Due to the Magnetic Field Forces as Observed by the Link Alignment System

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J.; Arce, J.; Barcala, J. M.; Calvo, E.; Ferrando, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.; Brochero, J.; Calderon, A.; Fernandez, M. G.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martinez-Ribero, C.; Matorras, F.; Rodrigo, T.; Rui-Arbol, P.; Scodellaro, L.; Sobron, M.; Vila, I.; Virto, A. L.; Fernandez, J.

    2010-05-01

    This document describes results obtained from the Link Alignment System data recorded during the CMS Magnet Test (at SX5 on ground Hall) and the CRAFT08 and 09 periods data taking in the point P5 (UX5), 100 m underground. A brief description of the system is followed by the discussion of the detected relative displacements (from micrometres to centimetres) between detector elements and rotation of detector structures (from microradiants to milliradiants). Observed motions are studied as functions of the magnetic fi eld intensity. Comparisons between recorded data on and under ground are made. (Author) 23 refs.

  4. The CMS Experiment: on and under Ground Motions of Structures Due to the Magnetic Field Forces as Observed by the Link Alignment System

    International Nuclear Information System (INIS)

    Alberdi, J.; Arce, J.; Barcala, J. M.; Calvo, E.; Ferrando, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.; Brochero, J.; Calderon, A.; Fernandez, M. G.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martinez-Ribero, C.; Matorras, F.; Rodrigo, T.; Rui-Arbol, P.; Scodellaro, L.; Sobron, M.; Vila, I.; Virto, A. L.; Fernandez, J.

    2010-01-01

    This document describes results obtained from the Link Alignment System data recorded during the CMS Magnet Test (at SX5 on ground Hall) and the CRAFT08 and 09 periods data taking in the point P5 (UX5), 100 m underground. A brief description of the system is followed by the discussion of the detected relative displacements (from micrometres to centimetres) between detector elements and rotation of detector structures (from microradiants to milliradiants). Observed motions are studied as functions of the magnetic fi eld intensity. Comparisons between recorded data on and under ground are made. (Author) 23 refs.

  5. Motions of CMS Detector Structures as Observed by the Link Alignment System during the Test of the 4 Tesla Magnet Solenoid

    International Nuclear Information System (INIS)

    Alberdi, J.; Arce, P.; Barcala, J. M.; Calvo, E.; Ferrando, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.; Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martin-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Scodellaro, L.; Sobron, M.; Vila, I.; Virto, A. L.

    2008-01-01

    This document describes results obtained from the Link Alignment System data recorded during the CMS Magnet Test. A brief description of the system is followed by the discussion of the detected relative displacements (from micro metres to centimetres) between detector elements and rotation of detector structures (from microradiants to milliradiants). Observed displacements are studied as functions of the magnetic fi eld intensity. In addition, a comparison of the reconstructed position of active element sensors with respect to their position as measured by photogrammetry is made and the reconstructed motions due to the magnetic field strength are described. (Author) 19 refs

  6. Motions of CMS detector structures due to the magnetic field forces as observed by the Link alignment system during the test of the 4 T magnet solenoid

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Moral, L.A.; Gomez, G.; Gonzalez-Sanchez, F.J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Martinez, P.; Scodellaro, L.; Vila, I.; Virto, A.L. [Instituto de Fisica de Cantabria (IFCA), CSIC-Universidad de Cantabria, Santander (Spain); Sobron, M. [Instituto de Fisica de Cantabria (IFCA), CSIC-Universidad de Cantabria, Santander (Spain)], E-mail: sobron@ifca.unican.es; Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M.I.; Molinero, A.; Navarrete, J.; Oller, J.C. [Centro de Investigaciones Energeticas Medioambientales y Tecnologicas (CIEMAT), Madrid (Spain)] (and others)

    2009-07-21

    This document describes results obtained from the Link alignment system data recorded during the Compact Muon Solenoid (CMS) Magnet Test. A brief description of the system is followed by a discussion of the detected relative displacements (from micrometres to centimetres) between detector elements and rotations of detector structures (from microradians to milliradians). Observed displacements are studied as functions of the magnetic field intensity. In addition, the reconstructed positions of active element sensors are compared to their positions as measured by photogrammetry and the reconstructed motions due to the magnetic field strength are described.

  7. Motions of CMS detector structures due to the magnetic field forces as observed by the Link alignment system during the test of the 4 T magnet solenoid

    International Nuclear Information System (INIS)

    Garcia-Moral, L.A.; Gomez, G.; Gonzalez-Sanchez, F.J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Martinez, P.; Scodellaro, L.; Vila, I.; Virto, A.L.; Sobron, M.; Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M.I.; Molinero, A.; Navarrete, J.; Oller, J.C.

    2009-01-01

    This document describes results obtained from the Link alignment system data recorded during the Compact Muon Solenoid (CMS) Magnet Test. A brief description of the system is followed by a discussion of the detected relative displacements (from micrometres to centimetres) between detector elements and rotations of detector structures (from microradians to milliradians). Observed displacements are studied as functions of the magnetic field intensity. In addition, the reconstructed positions of active element sensors are compared to their positions as measured by photogrammetry and the reconstructed motions due to the magnetic field strength are described.

  8. Querying archetype-based EHRs by search ontology-based XPath engineering.

    Science.gov (United States)

    Kropf, Stefan; Uciteli, Alexandr; Schierle, Katrin; Krücken, Peter; Denecke, Kerstin; Herre, Heinrich

    2018-05-11

    Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards. The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist. The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.

  9. A self-consistent two-dimensional resistive fluid theory of field-aligned potential structures including charge separation and magnetic and velocity shear

    International Nuclear Information System (INIS)

    Hesse, M.; Birn, J.; Schindler, K.

    1990-01-01

    A self-consistent two-fluid theory that includes the magnetic field and shear patterns therein is developed to model stationary electrostatic structures with field-aligned potential drops. Shear flow is also included in the theory since this seems to be a prominent feature of the structures of interest. In addition, Ohmic dissipation, a Hall term and pressure gradients in a generalized Ohm's law, modified for cases without quasi-neutrality are included. In the analytic theory, the electrostatic force is balanced by field-aligned pressure gradients, i.e., thermal effects in the direction of the magnetic field, and by pressure gradients and magnetic stresses in the perpendicular direction. Within this theory simple examples of applications are presented to demonstrate the kind of solutions resulting from the model. The results show how the effects of charge separation and shear in the magnetic field and the velocity can be combined to form self-consistent structures such as are found to exist above the aurora, suggested also in association with solar flares

  10. Structural and photoluminescence properties of aligned Sb-doped ZnO nanocolumns synthesized by the hydrothermal method

    Energy Technology Data Exchange (ETDEWEB)

    Fang Xuan [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China); Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Li Jinhua [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China); Zhao Dongxu, E-mail: dxzhao2000@yahoo.com.c [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Li Binghui; Zhang Zhenzhong; Shen Dezhen [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic Zone Changchun, 130033 (China); Wang Xiaohua; Wei Zhipeng [School of Science, Changchun University of Science and Technology, 7089-WeiXing Road, Changchun, 130022 (China)

    2010-08-02

    Aligned Sb-doped ZnO nanocolumns were synthesized by a simple hydrothermal method. Based on the analyses of the X-ray diffraction and photoluminescence result, it could be confirmed that the Sb has successfully doped in the ZnO crystal lattices to form an accepter energy level. At 85 K, the recombination of the acceptor-bound exciton was predominant in PL spectrum, which was attributed to the transition of the (Sb{sub Zn}-2V{sub Zn}) complex bound exciton. The acceptor binding energy had been calculated to be 123 meV.

  11. Structural and photoluminescence properties of aligned Sb-doped ZnO nanocolumns synthesized by the hydrothermal method

    International Nuclear Information System (INIS)

    Fang Xuan; Li Jinhua; Zhao Dongxu; Li Binghui; Zhang Zhenzhong; Shen Dezhen; Wang Xiaohua; Wei Zhipeng

    2010-01-01

    Aligned Sb-doped ZnO nanocolumns were synthesized by a simple hydrothermal method. Based on the analyses of the X-ray diffraction and photoluminescence result, it could be confirmed that the Sb has successfully doped in the ZnO crystal lattices to form an accepter energy level. At 85 K, the recombination of the acceptor-bound exciton was predominant in PL spectrum, which was attributed to the transition of the (Sb Zn -2V Zn ) complex bound exciton. The acceptor binding energy had been calculated to be 123 meV.

  12. Ontology for Semantic Data Integration in the Domain of IT Benchmarking.

    Science.gov (United States)

    Pfaff, Matthias; Neubig, Stefan; Krcmar, Helmut

    2018-01-01

    A domain-specific ontology for IT benchmarking has been developed to bridge the gap between a systematic characterization of IT services and their data-based valuation. Since information is generally collected during a benchmark exercise using questionnaires on a broad range of topics, such as employee costs, software licensing costs, and quantities of hardware, it is commonly stored as natural language text; thus, this information is stored in an intrinsically unstructured form. Although these data form the basis for identifying potentials for IT cost reductions, neither a uniform description of any measured parameters nor the relationship between such parameters exists. Hence, this work proposes an ontology for the domain of IT benchmarking, available at https://w3id.org/bmontology. The design of this ontology is based on requirements mainly elicited from a domain analysis, which considers analyzing documents and interviews with representatives from Small- and Medium-Sized Enterprises and Information and Communications Technology companies over the last eight years. The development of the ontology and its main concepts is described in detail (i.e., the conceptualization of benchmarking events, questionnaires, IT services, indicators and their values) together with its alignment with the DOLCE-UltraLite foundational ontology.

  13. Concepts, ontologies, and knowledge representation

    CERN Document Server

    Jakus, Grega; Omerovic, Sanida; Tomažic, Sašo

    2013-01-01

    Recording knowledge in a common framework that would make it possible to seamlessly share global knowledge remains an important challenge for researchers. This brief examines several ideas about the representation of knowledge addressing this challenge. A widespread general agreement is followed that states uniform knowledge representation should be achievable by using ontologies populated with concepts. A separate chapter is dedicated to each of the three introduced topics, following a uniform outline: definition, organization, and use. This brief is intended for those who want to get to know

  14. Nosology, ontology and promiscuous realism.

    Science.gov (United States)

    Binney, Nicholas

    2015-06-01

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

  15. Ontology modeling for generation of clinical pathways

    Directory of Open Access Journals (Sweden)

    Jasmine Tehrani

    2012-12-01

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

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

    Science.gov (United States)

    Figdor, Carrie

    2011-04-01

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

  17. New concepts for building vocabulary for cell image ontologies.

    Science.gov (United States)

    Plant, Anne L; Elliott, John T; Bhat, Talapady N

    2011-12-21

    There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical operations. Organizing metadata for cell imaging

  18. New concepts for building vocabulary for cell image ontologies

    Directory of Open Access Journals (Sweden)

    Plant Anne L

    2011-12-01

    Full Text Available Abstract Background There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Results Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical

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

    Science.gov (United States)

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

    2017-01-01

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

  20. Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

    Science.gov (United States)

    Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

    2015-07-28

    The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.