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Sample records for ontology analysis identifies

  1. Onto-clust--a methodology for combining clustering analysis and ontological methods for identifying groups of comorbidities for developmental disorders.

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    Peleg, Mor; Asbeh, Nuaman; Kuflik, Tsvi; Schertz, Mitchell

    2009-02-01

    Children with developmental disorders usually exhibit multiple developmental problems (comorbidities). Hence, such diagnosis needs to revolve on developmental disorder groups. Our objective is to systematically identify developmental disorder groups and represent them in an ontology. We developed a methodology that combines two methods (1) a literature-based ontology that we created, which represents developmental disorders and potential developmental disorder groups, and (2) clustering for detecting comorbid developmental disorders in patient data. The ontology is used to interpret and improve clustering results and the clustering results are used to validate the ontology and suggest directions for its development. We evaluated our methodology by applying it to data of 1175 patients from a child development clinic. We demonstrated that the ontology improves clustering results, bringing them closer to an expert generated gold-standard. We have shown that our methodology successfully combines an ontology with a clustering method to support systematic identification and representation of developmental disorder groups.

  2. Social Learning Network Analysis Model to Identify Learning Patterns Using Ontology Clustering Techniques and Meaningful Learning

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    Firdausiah Mansur, Andi Besse; Yusof, Norazah

    2013-01-01

    Clustering on Social Learning Network still not explored widely, especially when the network focuses on e-learning system. Any conventional methods are not really suitable for the e-learning data. SNA requires content analysis, which involves human intervention and need to be carried out manually. Some of the previous clustering techniques need…

  3. Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer.

    Science.gov (United States)

    Lando, Malin; Holden, Marit; Bergersen, Linn C; Svendsrud, Debbie H; Stokke, Trond; Sundfør, Kolbein; Glad, Ingrid K; Kristensen, Gunnar B; Lyng, Heidi

    2009-11-01

    Integrative analysis of gene dosage, expression, and ontology (GO) data was performed to discover driver genes in the carcinogenesis and chemoradioresistance of cervical cancers. Gene dosage and expression profiles of 102 locally advanced cervical cancers were generated by microarray techniques. Fifty-two of these patients were also analyzed with the Illumina expression method to confirm the gene expression results. An independent cohort of 41 patients was used for validation of gene expressions associated with clinical outcome. Statistical analysis identified 29 recurrent gains and losses and 3 losses (on 3p, 13q, 21q) associated with poor outcome after chemoradiotherapy. The intratumor heterogeneity, assessed from the gene dosage profiles, was low for these alterations, showing that they had emerged prior to many other alterations and probably were early events in carcinogenesis. Integration of the alterations with gene expression and GO data identified genes that were regulated by the alterations and revealed five biological processes that were significantly overrepresented among the affected genes: apoptosis, metabolism, macromolecule localization, translation, and transcription. Four genes on 3p (RYBP, GBE1) and 13q (FAM48A, MED4) correlated with outcome at both the gene dosage and expression level and were satisfactorily validated in the independent cohort. These integrated analyses yielded 57 candidate drivers of 24 genetic events, including novel loci responsible for chemoradioresistance. Further mapping of the connections among genetic events, drivers, and biological processes suggested that each individual event stimulates specific processes in carcinogenesis through the coordinated control of multiple genes. The present results may provide novel therapeutic opportunities of both early and advanced stage cervical cancers.

  4. Markov Chain Ontology Analysis (MCOA)

    Science.gov (United States)

    2012-01-01

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

  5. Identifying Granularity Differences between Large Biomedical Ontologies through Rules.

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    Sun, Pengfei; Zhang, Songmao

    2010-11-13

    The objective of this study is to identify the granularity differences as well as similarity between large biomedical ontologies through rules. Two anatomical ontologies were selected, and based on a set of concept mappings obtained through simple string matching techniques, we constructed rules to distinguish among different types of subclasses and classifications. 82% of the concept mappings have exactly the same classification in subclasses between the two ontologies. Other mappings are classified in different granularity, including additional subclasses, detailed classification, and different intermediate classification concepts. Using rules and the rule inference engine enables an automatic and scalable investigation of the structural incompatibility among biomedical ontologies.

  6. Ontology Maintenance using Textual Analysis

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    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.

  7. Ontology Maintenance using Textual Analysis

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    Yassine Gargouri

    2003-10-01

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

  8. Terminological Ontologies for Risk and Vulnerability Analysis

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2014-01-01

    Risk and vulnerability analyses are an important preliminary stage in civil contingency planning. The Danish Emergency Management Agency has developed a generic model and a set of tools that may be used in the preparedness planning, i.e. for identifying and describing society’s critical functions......, for formulating threat scenarios and for assessing consequences. Terminological ontologies, which are systems of domain specific concepts comprising concept relations and characteristics, are useful, both when describing the central concepts of risk and vulnerability analysis (meta concepts), and for further...... structuring and enriching the taxonomies of society’s critical functions and threats, which form an important part of the model. Creating terminological ontologies is a time consuming work, and therefore there is a need for automatic tools for extraction of terms, concept relations and characteristics...

  9. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.

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    Andreas Henschel

    2015-10-01

    Full Text Available Comprehensive mapping of environmental microbiomes in terms of their compositional features remains a great challenge in understanding the microbial biosphere of the Earth. It bears promise to identify the driving forces behind the observed community patterns and whether community assembly happens deterministically. Advances in Next Generation Sequencing allow large community profiling studies, exceeding sequencing data output of conventional methods in scale by orders of magnitude. However, appropriate collection systems are still in a nascent state. We here present a database of 20,427 diverse environmental 16S rRNA profiles from 2,426 independent studies, which forms the foundation of our meta-analysis. We conducted a sample size adaptive all-against-all beta diversity comparison while also respecting phylogenetic relationships of Operational Taxonomic Units(OTUs. After conventional hierarchical clustering we systematically test for enrichment of Environmental Ontology terms and their abstractions in all possible clusters. This post-hoc algorithm provides a novel formalism that quantifies to what extend compositional and semantic similarity of microbial community samples coincide. We automatically visualize significantly enriched subclusters on a comprehensive dendrogram of microbial communities. As a result we obtain the hitherto most differentiated and comprehensive view on global patterns of microbial community diversity. We observe strong clusterability of microbial communities in ecosystems such as human/mammal-associated, geothermal, fresh water, plant-associated, soils and rhizosphere microbiomes, whereas hypersaline and anthropogenic samples are less homogeneous. Moreover, saline samples appear less cohesive in terms of compositional properties than previously reported.

  10. 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.

  11. Ontological Modeling for Integrated Spacecraft Analysis

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    Wicks, Erica

    2011-01-01

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

  12. POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.

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    Shameer, Khader; Naika, Mahantesha Bn; Mathew, Oommen K; Sowdhamini, Ramanathan

    2014-01-01

    Biological enrichment analysis using gene ontology (GO) provides a global overview of the functional role of genes or proteins identified from large-scale genomic or proteomic experiments. Phenomic enrichment analysis of gene lists can provide an important layer of information as well as cellular components, molecular functions, and biological processes associated with gene lists. Plant phenomic enrichment analysis will be useful for performing new experiments to better understand plant systems and for the interpretation of gene or proteins identified from high-throughput experiments. Plant ontology (PO) is a compendium of terms to define the diverse phenotypic characteristics of plant species, including plant anatomy, morphology, and development stages. Adoption of this highly useful ontology is limited, when compared to GO, because of the lack of user-friendly tools that enable the use of PO for statistical enrichment analysis. To address this challenge, we introduce Plant Ontology Enrichment Analysis Server (POEAS) in the public domain. POEAS uses a simple list of genes as input data and performs enrichment analysis using Ontologizer 2.0 to provide results in two levels, enrichment results and visualization utilities, to generate ontological graphs that are of publication quality. POEAS also offers interactive options to identify user-defined background population sets, various multiple-testing correction methods, different enrichment calculation methods, and resampling tests to improve statistical significance. The availability of such a tool to perform phenomic enrichment analyses using plant genes as a complementary resource will permit the adoption of PO-based phenomic analysis as part of analytical workflows. POEAS can be accessed using the URL http://caps.ncbs.res.in/poeas.

  13. An empirical analysis of ontology reuse in BioPortal.

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

    2017-07-01

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

  14. Identifying redundant and missing relations in the gene ontology.

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    Mougin, Fleur

    2015-01-01

    Significant efforts have been undertaken for providing the Gene Ontology (GO) in a computable format as well as for enriching it with logical definitions. Automated approaches can thus be applied to GO for assisting its maintenance and for checking its internal coherence. However, inconsistencies may still remain within GO. In this frame, the objective of this work was to audit GO relationships. First, reasoning over relationships was exploited for detecting redundant relations existing between GO concepts. Missing necessary and sufficient conditions were then identified based on the compositional structure of the preferred names of GO concepts. More than one thousand redundant relations and 500 missing necessary and sufficient conditions were found. The proposed approach was thus successful for detecting inconsistencies within GO relations. The application of lexical approaches as well as the exploitation of synonyms and textual definitions could be useful for identifying additional necessary and sufficient conditions. Multiple necessary and sufficient conditions for a given GO concept may be indicative of inconsistencies.

  15. [Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

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    Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

    2012-07-01

    In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

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

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    Irena ATANASOVA

    2011-01-01

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

  17. Ontology integration to identify protein complex in protein interaction networks

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    Yang Zhihao

    2011-10-01

    Full Text Available Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity method, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes. Results The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.

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

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

    2017-09-06

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

  19. Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE.

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    Duque-Ramos, Astrid; Quesada-Martínez, Manuel; Iniesta-Moreno, Miguela; Fernández-Breis, Jesualdo Tomás; Stevens, Robert

    2016-10-17

    The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly and frequently published in ontology repositories. This has the implication of there being a high number of ontology versions over a short time span. Given this level of activity, ontology designers need to be supported in the effective management of the evolution of biomedical ontologies as the different changes may affect the engineering and quality of the ontology. This is why there is a need for methods that contribute to the analysis of the effects of changes and evolution of ontologies. In this paper we approach this issue from the ontology quality perspective. In previous work we have developed an ontology evaluation framework based on quantitative metrics, called OQuaRE. Here, OQuaRE is used as a core component in a method that enables the analysis of the different versions of biomedical ontologies using the quality dimensions included in OQuaRE. Moreover, we describe and use two scales for evaluating the changes between the versions of a given ontology. The first one is the static scale used in OQuaRE and the second one is a new, dynamic scale, based on the observed values of the quality metrics of a corpus defined by all the versions of a given ontology (life-cycle). In this work we explain how OQuaRE can be adapted for understanding the evolution of ontologies. Its use has been illustrated with the ontology of bioinformatics operations, types of data, formats, and topics (EDAM). The two scales included in OQuaRE provide complementary information about the evolution of the ontologies. The application of the static scale, which is the original OQuaRE scale, to the versions of the EDAM ontology reveals a design based on good ontological engineering principles. The application of the dynamic scale has enabled a more detailed analysis of the evolution of

  20. Ontology-Based Analysis of Microarray Data.

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    Giuseppe, Agapito; Milano, Marianna

    2016-01-01

    The importance of semantic-based methods and algorithms for the analysis and management of biological data is growing for two main reasons. From a biological side, knowledge contained in ontologies is more and more accurate and complete, from a computational side, recent algorithms are using in a valuable way such knowledge. Here we focus on semantic-based management and analysis of protein interaction networks referring to all the approaches of analysis of protein-protein interaction data that uses knowledge encoded into biological ontologies. Semantic approaches for studying high-throughput data have been largely used in the past to mine genomic and expression data. Recently, the emergence of network approaches for investigating molecular machineries has stimulated in a parallel way the introduction of semantic-based techniques for analysis and management of network data. The application of these computational approaches to the study of microarray data can broad the application scenario of them and simultaneously can help the understanding of disease development and progress.

  1. A bibliometric and visual analysis of global geo-ontology research

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    Li, Lin; Liu, Yu; Zhu, Haihong; Ying, Shen; Luo, Qinyao; Luo, Heng; Kuai, Xi; Xia, Hui; Shen, Hang

    2017-02-01

    In this paper, the results of a bibliometric and visual analysis of geo-ontology research articles collected from the Web of Science (WOS) database between 1999 and 2014 are presented. The numbers of national institutions and published papers are visualized and a global research heat map is drawn, illustrating an overview of global geo-ontology research. In addition, we present a chord diagram of countries and perform a visual cluster analysis of a knowledge co-citation network of references, disclosing potential academic communities and identifying key points, main research areas, and future research trends. The International Journal of Geographical Information Science, Progress in Human Geography, and Computers & Geosciences are the most active journals. The USA makes the largest contributions to geo-ontology research by virtue of its highest numbers of independent and collaborative papers, and its dominance was also confirmed in the country chord diagram. The majority of institutions are in the USA, Western Europe, and Eastern Asia. Wuhan University, University of Munster, and the Chinese Academy of Sciences are notable geo-ontology institutions. Keywords such as "Semantic Web," "GIS," and "space" have attracted a great deal of attention. "Semantic granularity in ontology-driven geographic information systems, "Ontologies in support of activities in geographical space" and "A translation approach to portable ontology specifications" have the highest cited centrality. Geographical space, computer-human interaction, and ontology cognition are the three main research areas of geo-ontology. The semantic mismatch between the producers and users of ontology data as well as error propagation in interdisciplinary and cross-linguistic data reuse needs to be solved. In addition, the development of geo-ontology modeling primitives based on OWL (Web Ontology Language)and finding methods to automatically rework data in Semantic Web are needed. Furthermore, the topological

  2. Analysis of the OWL ontologies: A survey

    OpenAIRE

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

    2011-01-01

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

  3. Development and Evaluation of an Obesity Ontology for Social Big Data Analysis.

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    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.

  4. Onto-CC: a web server for identifying Gene Ontology conceptual clusters

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    Romero-Zaliz, R.; del Val, C.; Cobb, J. P.; Zwir, I.

    2008-01-01

    The Gene Ontology (GO) vocabulary has been extensively explored to analyze the functions of coexpressed genes. However, despite its extended use in Biology and Medical Sciences, there are still high levels of uncertainty about which ontology (i.e. Molecular Process, Cellular Component or Molecular Function) should be used, and at which level of specificity. Moreover, the GO database can contain incomplete information resulting from human annotations, or highly influenced by the available knowledge about a specific branch in an ontology. In spite of these drawbacks, there is a trend to ignore these problems and even use GO terms to conduct searches of gene expression profiles (i.e. expression + GO) instead of more cautious approaches that just consider them as an independent source of validation (i.e. expression versus GO). Consequently, propagating the uncertainty and producing biased analysis of the required gene grouping hypotheses. We proposed a web tool, Onto-CC, as an automatic method specially suited for independent explanation/validation of gene grouping hypotheses (e.g. coexpressed genes) based on GO clusters (i.e. expression versus GO). Onto-CC approach reduces the uncertainty of the queries by identifying optimal conceptual clusters that combine terms from different ontologies simultaneously, as well as terms defined at different levels of specificity in the GO hierarchy. To do so, we implemented the EMO-CC methodology to find clusters in structural databases [GO Directed acyclic Graph (DAG) tree], inspired on Conceptual Clustering algorithms. This approach allows the management of optimal cluster sets as potential parallel hypotheses, guided by multiobjective/multimodal optimization techniques. Therefore, we can generate alternative and, still, optimal explanations of queries that can provide new insights for a given problem. Onto-CC has been successfully used to test different medical and biological hypotheses including the explanation and prediction of

  5. Classification analysis of microarray data based on ontological engineering

    Institute of Scientific and Technical Information of China (English)

    LI Guo-qi; SHENG Huan-ye

    2007-01-01

    Background knowledge is important for data mining, especially in complicated situation. Ontological engineering is the successor of knowledge engineering. The sharable knowledge bases built on ontology can be used to provide background knowledge to direct the process of data mining. This paper gives a common introduction to the method and presents a practical analysis example using SVM (support vector machine) as the classifier. Gene Ontology and the accompanying annotations compose a big knowledge base, on which many researches have been carried out. Microarray dataset is the output of DNA chip.With the help of Gene Ontology we present a more elaborate analysis on microarray data than former researchers. The method can also be used in other fields with similar scenario.

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

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

    2017-09-05

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

  7. Non-lexical approaches to identifying associative relations in the gene ontology.

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    Bodenreider, Olivier; Aubry, Marc; Burgun, Anita

    2005-01-01

    The Gene Ontology (GO) is a controlled vocabulary widely used for the annotation of gene products. GO is organized in three hierarchies for molecular functions, cellular components, and biological processes but no relations are provided among terms across hierarchies. The objective of this study is to investigate three non-lexical approaches to identifying such associative relations in GO and compare them among themselves and to lexical approaches. The three approaches are: computing similarity in a vector space model, statistical analysis of co-occurrence of GO terms in annotation databases, and association rule mining. Five annotation databases (FlyBase, the Human subset of GOA, MGI, SGD, and WormBase) are used in this study. A total of 7,665 associations were identified by at least one of the three non-lexical approaches. Of these, 12% were identified by more than one approach. While there are almost 6,000 lexical relations among GO terms, only 203 associations were identified by both non-lexical and lexical approaches. The associations identified in this study could serve as the starting point for adding associative relations across hierarchies to GO, but would require manual curation. The application to quality assurance of annotation databases is also discussed.

  8. GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology

    Directory of Open Access Journals (Sweden)

    Yang Da

    2007-01-01

    Full Text Available Abstract Background Rapid progress in high-throughput biotechnologies (e.g. microarrays and exponential accumulation of gene functional knowledge make it promising for systematic understanding of complex human diseases at functional modules level. Based on Gene Ontology, a large number of automatic tools have been developed for the functional analysis and biological interpretation of the high-throughput microarray data. Results Different from the existing tools such as Onto-Express and FatiGO, we develop a tool named GO-2D for identifying 2-dimensional functional modules based on combined GO categories. For example, it refines biological process categories by sorting their genes into different cellular component categories, and then extracts those combined categories enriched with the interesting genes (e.g., the differentially expressed genes for identifying the cellular-localized functional modules. Applications of GO-2D to the analyses of two human cancer datasets show that very specific disease-relevant processes can be identified by using cellular location information. Conclusion For studying complex human diseases, GO-2D can extract functionally compact and detailed modules such as the cellular-localized ones, characterizing disease-relevant modules in terms of both biological processes and cellular locations. The application results clearly demonstrate that 2-dimensional approach complementary to current 1-dimensional approach is powerful for finding modules highly relevant to diseases.

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

    Science.gov (United States)

    Hieb, Jeffrey; Graham, James; Guan, Jian

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

  10. Constructing Ontology for Knowledge Sharing of Materials Failure Analysis

    Directory of Open Access Journals (Sweden)

    Peng Shi

    2014-01-01

    Full Text Available Materials failure indicates the fault with materials or components during their performance. To avoid the reoccurrence of similar failures, materials failure analysis is executed to investigate the reasons for the failure and to propose improved strategies. The whole procedure needs sufficient domain knowledge and also produces valuable new knowledge. However, the information about the materials failure analysis is usually retained by the domain expert, and its sharing is technically difficult. This phenomenon may seriously reduce the efficiency and decrease the veracity of the failure analysis. To solve this problem, this paper adopts ontology, a novel technology from the Semantic Web, as a tool for knowledge representation and sharing and describes the construction of the ontology to obtain information concerning the failure analysis, application area, materials, and failure cases. The ontology represented information is machine-understandable and can be easily shared through the Internet. At the same time, failure case intelligent retrieval, advanced statistics, and even automatic reasoning can be accomplished based on ontology represented knowledge. Obviously this can promote the knowledge sharing of materials service safety and improve the efficiency of failure analysis. The case of a nuclear power plant area is presented to show the details and benefits of this method.

  11. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

    Science.gov (United States)

    Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

    2013-01-01

    Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

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

    OpenAIRE

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

    2015-01-01

    Background 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,...

  13. Sentiment analysis and ontology engineering an environment of computational intelligence

    CERN Document Server

    Chen, Shyi-Ming

    2016-01-01

    This edited volume provides the reader with a fully updated, in-depth treatise on the emerging principles, conceptual underpinnings, algorithms and practice of Computational Intelligence in the realization of concepts and implementation of models of sentiment analysis and ontology –oriented engineering. The volume involves studies devoted to key issues of sentiment analysis, sentiment models, and ontology engineering. The book is structured into three main parts. The first part offers a comprehensive and prudently structured exposure to the fundamentals of sentiment analysis and natural language processing. The second part consists of studies devoted to the concepts, methodologies, and algorithmic developments elaborating on fuzzy linguistic aggregation to emotion analysis, carrying out interpretability of computational sentiment models, emotion classification, sentiment-oriented information retrieval, a methodology of adaptive dynamics in knowledge acquisition. The third part includes a plethora of applica...

  14. Transcriptome Sequencing Identified Genes and Gene Ontologies Associated with Early Freezing Tolerance in Maize

    Science.gov (United States)

    Li, Zhao; Hu, Guanghui; Liu, Xiangfeng; Zhou, Yao; Li, Yu; Zhang, Xu; Yuan, Xiaohui; Zhang, Qian; Yang, Deguang; Wang, Tianyu; Zhang, Zhiwu

    2016-01-01

    Originating in a tropical climate, maize has faced great challenges as cultivation has expanded to the majority of the world's temperate zones. In these zones, frost and cold temperatures are major factors that prevent maize from reaching its full yield potential. Among 30 elite maize inbred lines adapted to northern China, we identified two lines of extreme, but opposite, freezing tolerance levels—highly tolerant and highly sensitive. During the seedling stage of these two lines, we used RNA-seq to measure changes in maize whole genome transcriptome before and after freezing treatment. In total, 19,794 genes were expressed, of which 4550 exhibited differential expression due to either treatment (before or after freezing) or line type (tolerant or sensitive). Of the 4550 differently expressed genes, 948 exhibited differential expression due to treatment within line or lines under freezing condition. Analysis of gene ontology found that these 948 genes were significantly enriched for binding functions (DNA binding, ATP binding, and metal ion binding), protein kinase activity, and peptidase activity. Based on their enrichment, literature support, and significant levels of differential expression, 30 of these 948 genes were selected for quantitative real-time PCR (qRT-PCR) validation. The validation confirmed our RNA-Seq-based findings, with squared correlation coefficients of 80% and 50% in the tolerance and sensitive lines, respectively. This study provided valuable resources for further studies to enhance understanding of the molecular mechanisms underlying maize early freezing response and enable targeted breeding strategies for developing varieties with superior frost resistance to achieve yield potential. PMID:27774095

  15. Initial implementation of a comparative data analysis ontology.

    Science.gov (United States)

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

    2009-07-03

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

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

    Science.gov (United States)

    2013-01-01

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

  17. Initial Implementation of a comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-01-01

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

  18. Initial Implementation of a Comparative Data Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    2009-07-01

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

  19. ProKinO: an ontology for integrative analysis of protein kinases in cancer.

    Directory of Open Access Journals (Sweden)

    Gurinder Gosal

    Full Text Available BACKGROUND: Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats. RESULTS: Here, we describe ProKinO, a protein kinase-specific ontology, which provides a controlled vocabulary of terms, their hierarchy, and relationships unifying sequence, structure, function, mutation and pathway information on protein kinases. The conceptual representation of such diverse forms of information in one place not only allows rapid discovery of significant information related to a specific protein kinase, but also enables large-scale integrative analysis of protein kinase data in ways not possible through other kinase-specific resources. We have performed several integrative analyses of ProKinO data and, as an example, found that a large number of somatic mutations (∼288 distinct mutations associated with the haematopoietic neoplasm cancer type map to only 8 kinases in the human kinome. This is in contrast to glioma, where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations. CONCLUSION: We present an integrated framework for large-scale integrative analysis of protein kinase data. Navigation and analysis of ontology data can be performed using the ontology browser available at: http://vulcan.cs.uga.edu/prokino.

  20. 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

  1. Persistent identifiers for web service requests relying on a provenance ontology design pattern

    Science.gov (United States)

    Car, Nicholas; Wang, Jingbo; Wyborn, Lesley; Si, Wei

    2016-04-01

    Delivering provenance information for datasets produced from static inputs is relatively straightforward: we represent the processing actions and data flow using provenance ontologies and link to stored copies of the inputs stored in repositories. If appropriate detail is given, the provenance information can then describe what actions have occurred (transparency) and enable reproducibility. When web service-generated data is used by a process to create a dataset instead of a static inputs, we need to use sophisticated provenance representations of the web service request as we can no longer just link to data stored in a repository. A graph-based provenance representation, such as the W3C's PROV standard, can be used to model the web service request as a single conceptual dataset and also as a small workflow with a number of components within the same provenance report. This dual representation does more than just allow simplified or detailed views of a dataset's production to be used where appropriate. It also allow persistent identifiers to be assigned to instances of a web service requests, thus enabling one form of dynamic data citation, and for those identifiers to resolve to whatever level of detail implementers think appropriate in order for that web service request to be reproduced. In this presentation we detail our reasoning in representing web service requests as small workflows. In outline, this stems from the idea that web service requests are perdurant things and in order to most easily persist knowledge of them for provenance, we should represent them as a nexus of relationships between endurant things, such as datasets and knowledge of particular system types, as these endurant things are far easier to persist. We also describe the ontology design pattern that we use to represent workflows in general and how we apply it to different types of web service requests. We give examples of specific web service requests instances that were made by systems

  2. Extending TOPS: Ontology-driven Anomaly Detection and Analysis System

    Science.gov (United States)

    Votava, P.; Nemani, R. R.; Michaelis, A.

    2010-12-01

    Terrestrial Observation and Prediction System (TOPS) is a flexible modeling software system that integrates ecosystem models with frequent satellite and surface weather observations to produce ecosystem nowcasts (assessments of current conditions) and forecasts useful in natural resources management, public health and disaster management. We have been extending the Terrestrial Observation and Prediction System (TOPS) to include a capability for automated anomaly detection and analysis of both on-line (streaming) and off-line data. In order to best capture the knowledge about data hierarchies, Earth science models and implied dependencies between anomalies and occurrences of observable events such as urbanization, deforestation, or fires, we have developed an ontology to serve as a knowledge base. We can query the knowledge base and answer questions about dataset compatibilities, similarities and dependencies so that we can, for example, automatically analyze similar datasets in order to verify a given anomaly occurrence in multiple data sources. We are further extending the system to go beyond anomaly detection towards reasoning about possible causes of anomalies that are also encoded in the knowledge base as either learned or implied knowledge. This enables us to scale up the analysis by eliminating a large number of anomalies early on during the processing by either failure to verify them from other sources, or matching them directly with other observable events without having to perform an extensive and time-consuming exploration and analysis. The knowledge is captured using OWL ontology language, where connections are defined in a schema that is later extended by including specific instances of datasets and models. The information is stored using Sesame server and is accessible through both Java API and web services using SeRQL and SPARQL query languages. Inference is provided using OWLIM component integrated with Sesame.

  3. The design ontology

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  4. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  5. Using Ontologies for Enterprise Architecture Integration and Analysis

    Directory of Open Access Journals (Sweden)

    Gonçalo Antunes

    2014-03-01

    Full Text Available Enterprise architecture facilitates the alignment between different domains, such as business, applications and information technology. These domains must be described with description languages that best address the concerns of its stakeholders. However, current model-based enterprise architecture techniques are unable to integrate multiple descriptions languages either due to the lack of suitable extension mechanisms or because they lack the means to maintain the coherence, consistency and traceability between the representations of the multiple domains of the enterprise. On the other hand, enterprise architecture models are often designed and used for communication and not for automated analysis of its contents. Model analysis is a valuable tool for assessing the qualities of a model, such as conformance and completeness, and also for supporting decision making. This paper addresses these two issues found in model-based enterprise architecture: (1 the integration of domain description languages, and (2 the automated analysis of models. This proposal uses ontology engineering techniques to specify and integrate the different domains and reasoning and querying as a means to analyse the models. The utility of the proposal is shown through an evaluation scenario that involve the analysis of an enterprise architecture model that spans multiple domains.

  6. Applying the functional abnormality ontology pattern to anatomical functions

    Directory of Open Access Journals (Sweden)

    Hoehndorf Robert

    2010-03-01

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

  7. CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Son Tran

    2011-04-01

    Full Text Available Abstract Background The Comparative Data Analysis Ontology (CDAO is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices. Results Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store. Conclusions CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore.

  8. 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.

  9. Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway.

    Science.gov (United States)

    Yang, Jing; Chen, Lei; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2014-01-01

    Cancer is a serious disease that causes many deaths every year. We urgently need to design effective treatments to cure this disease. Tumor suppressor genes (TSGs) are a type of gene that can protect cells from becoming cancerous. In view of this, correct identification of TSGs is an alternative method for identifying effective cancer therapies. In this study, we performed gene ontology (GO) and pathway enrichment analysis of the TSGs and non-TSGs. Some popular feature selection methods, including minimum redundancy maximum relevance (mRMR) and incremental feature selection (IFS), were employed to analyze the enrichment features. Accordingly, some GO terms and KEGG pathways, such as biological adhesion, cell cycle control, genomic stability maintenance and cell death regulation, were extracted, which are important factors for identifying TSGs. We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments.

  10. 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.

  11. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

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

  12. Exploring biomedical ontology mappings with graph theory methods.

    Science.gov (United States)

    Kocbek, Simon; Kim, Jin-Dong

    2017-01-01

    In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

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

    Directory of Open Access Journals (Sweden)

    Tao Cui

    2012-12-01

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

  14. A Simple Strategy to Start Domain Ontology from Scratch

    Directory of Open Access Journals (Sweden)

    Ivo Wolff Gersberg

    2014-01-01

    Full Text Available Aiming the usage of Domain Ontology as an educational tool for neophyte students and focusing in a fast and easy way to start Domain Ontology from scratch, the semantics are set aside to identify contexts of concepts (terms to build the ontology. Text Mining, Link Analysis and Graph Analysis create an abstract rough sketch of interactions between terms. This first rough sketch is presented to the expert providing insights into and inspires him to inform or communicate knowledge, through assertive sentences. Those assertive sentences subsidize the creation of the ontology. A web prototype tool to visualize the ontology and retrieve book contents is also presented.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    Groß, Anika; Pruski, Cédric; Rahm, Erhard

    2016-01-01

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

  17. The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

    Science.gov (United States)

    Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria; Lin, Yu; Hero, Alfred; Smith, Barry; He, Yongqun

    2016-09-14

    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms in OBCS including 'data collection', 'data transformation in statistics', 'data visualization', 'statistical data analysis', and 'drawing a conclusion based on data', cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. Currently, OBCS comprehends 878 terms, representing 20 BFO classes, 403 OBI classes, 229 OBCS specific classes, and 122 classes imported from ten other OBO ontologies. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. Other ongoing projects using OBCS for statistical data processing are also discussed. The OBCS source code and documentation are available at: https://github.com/obcs/obcs . The Ontology

  18. China’s National Health Policies: An Ontological Analysis

    Science.gov (United States)

    Dai, Guobin; Deng, Fang; Ramaprasad, Arkalgud; Syn, Thant

    2016-01-01

    The health care system in China is facing a multitude of challenges owing to the changing demographics of the country, the evolving economics of health care, and the emerging epidemiology of health as well as diseases. China’s many national health care policies are documented in Chinese text documents. It is necessary to map the policies synoptically, systemically, and systematically to discover their emphases and biases, assess them, and modify them in the future. Using a logically constructed ontology of health care policies based on the common bodies of knowledge as a lens, we map the current policies to reveal their ‘bright’, ‘light’, and ‘blind/blank’ spots. The ontological map will help (a) develop a roadmap for future health care policies in China, and (b) compare and contrast China’s health care policies with other countries’. PMID:28210417

  19. Ontology-based representation and analysis of host-Brucella interactions.

    Science.gov (United States)

    Lin, Yu; Xiang, Zuoshuang; He, Yongqun

    2015-01-01

    -Brucella interactions and implemented in IDOBRU. Current IDOBRU includes 3611 ontology terms. SPARQL queries identified many results that are critical to the host-Brucella interactions. For example, out of 269 protein virulence factors related to macrophage-Brucella interactions, 81 are critical to Brucella intracellular replication inside macrophages. A SPARQL query also identified 11 biological processes important for Brucella virulence. To systematically represent and analyze fundamental host-pathogen interaction mechanisms, we provided for the first time comprehensive ontological modeling of host-pathogen interactions using Brucella as the pathogen model. The methods and ontology representations used in our study are generic and can be broadened to study the interactions between hosts and other pathogens.

  20. Pre-incident Analysis using Multigraphs and Faceted Ontologies

    Science.gov (United States)

    2013-08-01

    device (IND), or can be used as a dispersal mechanism for a radiological dispersal device (RDD) attack. Hence, the common convention of dealing with...ontology for beverages, part of which is shown in the form of an entity- relationship (ER) graph in Figure 4. The entities Beer, Wine , etc. have is a...links to the entity Alcoholic Drinks. The entities Grapes and Grains have is a links to Plants. There is also a made from link from Wine to Grapes and

  1. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

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

    2009-01-01

    for producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

  2. 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 ...

  3. Air Pollution Analysis using Ontologies and Regression Models

    Directory of Open Access Journals (Sweden)

    Parul Choudhary

    2016-07-01

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

  4. 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.

  5. An Analysis of the Ontological Causal Relation in Physics and Its Educational Implications

    Science.gov (United States)

    Cheong, Yong Wook

    2016-08-01

    An ontological causal relation is a quantified relation between certain interactions and changes in corresponding properties. Key ideas in physics, such as Newton's second law and the first law of thermodynamics, are representative examples of these relations. In connection with the teaching and learning of these relations, this study investigated three issues: the appropriate view concerning ontological category, the role and status of ontological causal relations, and university students' understanding of the role and status of these relations. Concerning the issue of proper ontology, this study suggests an alternative view that distinguishes between interaction and property at the macroscopic level, in contrast to Chi and colleagues' influential view. Concerning the role and status of the relations, we conclude that fundamental ontological causal relations should be regarded as knowledge at the core of relevant physics theories. However, upon analysis of participants' responses, this study finds that university students' views on the status of the heat capacity relation and Newton's second law are quite different. Several possible educational implications of these results are discussed.

  6. An Earthquake Source Ontology for Seismic Hazard Analysis and Ground Motion Simulation

    Science.gov (United States)

    Zechar, J. D.; Jordan, T. H.; Gil, Y.; Ratnakar, V.

    2005-12-01

    Representation of the earthquake source is an important element in seismic hazard analysis and earthquake simulations. Source models span a range of conceptual complexity - from simple time-independent point sources to extended fault slip distributions. Further computational complexity arises because the seismological community has established so many source description formats and variations thereof; what this means is that conceptually equivalent source models are often expressed in different ways. Despite the resultant practical difficulties, there exists a rich semantic vocabulary for working with earthquake sources. For these reasons, we feel it is appropriate to create a semantic model of earthquake sources using an ontology, a computer science tool from the field of knowledge representation. Unlike the domain of most ontology work to date, earthquake sources can be described by a very precise mathematical framework. Another uniqueness associated with developing such an ontology is that earthquake sources are often used as computational objects. A seismologist generally wants more than to simply construct a source and have it be well-formed and properly described; additionally, the source will be used for performing calculations. Representation and manipulation of complex mathematical objects presents a challenge to the ontology development community. In order to enable simulations involving many different types of source models, we have completed preliminary development of a seismic point source ontology. The use of an ontology to represent knowledge provides machine interpretability and the ability to validate logical consistency and completeness. Our ontology, encoded using the OWL Web Ontology Language - a standard from the World Wide Web Consortium, contains the conceptual definitions and relationships necessary for source translation services. For example, specification of strike, dip, rake, and seismic moment will automatically translate into a double

  7. Ontologies in biological data visualization.

    Science.gov (United States)

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

    2014-01-01

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

  8. Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data.

    Science.gov (United States)

    Broadbent, J A; Sampson, D L; Broszczak, D A; Upton, Z; Huygens, F

    2015-05-01

    Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data. Copyright © 2015 Elsevier GmbH. All rights reserved.

  9. Ontological Analysis of Integrated Process Models: testing hypotheses

    Directory of Open Access Journals (Sweden)

    Michael Rosemann

    2001-11-01

    Full Text Available Integrated process modeling is achieving prominence in helping to document and manage business administration and IT processes in organizations. The ARIS framework is a popular example for a framework of integrated process modeling not least because it underlies the 800 or more reference models embedded in the world's most popular ERP package, SAP R/3. This paper demonstrates the usefulness of the Bunge-Wand-Weber (BWW representation model for evaluating modeling grammars such as those constituting ARIS. It reports some initial insights gained from pilot testing Green and Rosemann's (2000 evaluative propositions. Even when considering all five views of ARIS, modelers have problems representing business rules, the scope and boundary of systems, and decomposing models. However, even though it is completely ontologically redundant, users still find the function view useful in modeling.

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

    Science.gov (United States)

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

    2016-10-01

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

  11. Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Ryan M. Ames

    2017-01-01

    Full Text Available Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs, hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.

  12. A Framework for Geographic Object-Based Image Analysis (GEOBIA) based on geographic ontology

    Science.gov (United States)

    Gu, H. Y.; Li, H. T.; Yan, L.; Lu, X. J.

    2015-06-01

    GEOBIA (Geographic Object-Based Image Analysis) is not only a hot topic of current remote sensing and geographical research. It is believed to be a paradigm in remote sensing and GIScience. The lack of a systematic approach designed to conceptualize and formalize the class definitions makes GEOBIA a highly subjective and difficult method to reproduce. This paper aims to put forward a framework for GEOBIA based on geographic ontology theory, which could implement "Geographic entities - Image objects - Geographic objects" true reappearance. It consists of three steps, first, geographical entities are described by geographic ontology, second, semantic network model is built based on OWL(ontology web language), at last, geographical objects are classified with decision rule or other classifiers. A case study of farmland ontology was conducted for describing the framework. The strength of this framework is that it provides interpretation strategies and global framework for GEOBIA with the property of objective, overall, universal, universality, etc., which avoids inconsistencies caused by different experts' experience and provides an objective model for mage analysis.

  13. 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.

  14. Kuhn's Ontological Relativism.

    Science.gov (United States)

    Sankey, Howard

    2000-01-01

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

  15. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

    Science.gov (United States)

    Cibrián-Jaramillo, Angélica; De la Torre-Bárcena, Jose E; Lee, Ernest K; Katari, Manpreet S; Little, Damon P; Stevenson, Dennis W; Martienssen, Rob; Coruzzi, Gloria M; DeSalle, Rob

    2010-07-12

    We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.

  16. A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis.

    Science.gov (United States)

    Weber, Kristoffer; Bartsch, Udo; Stocking, Carol; Fehse, Boris

    2008-04-01

    Functional gene analysis requires the possibility of overexpression, as well as downregulation of one, or ideally several, potentially interacting genes. Lentiviral vectors are well suited for this purpose as they ensure stable expression of complementary DNAs (cDNAs), as well as short-hairpin RNAs (shRNAs), and can efficiently transduce a wide spectrum of cell targets when packaged within the coat proteins of other viruses. Here we introduce a multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors designed according to the "building blocks" principle. Using a wide spectrum of different fluorescent markers, including drug-selectable enhanced green fluorescent protein (eGFP)- and dTomato-blasticidin-S resistance fusion proteins, LeGO vectors allow simultaneous analysis of multiple genes and shRNAs of interest within single, easily identifiable cells. Furthermore, each functional module is flanked by unique cloning sites, ensuring flexibility and individual optimization. The efficacy of these vectors for analyzing multiple genes in a single cell was demonstrated in several different cell types, including hematopoietic, endothelial, and neural stem and progenitor cells, as well as hepatocytes. LeGO vectors thus represent a valuable tool for investigating gene networks using conditional ectopic expression and knock-down approaches simultaneously.

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

    Science.gov (United States)

    2011-01-01

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

  18. Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network.

    Science.gov (United States)

    Karadeniz, İlknur; Hur, Junguk; He, Yongqun; Özgür, Arzucan

    2015-01-01

    Brucella is an intracellular bacterium that causes chronic brucellosis in humans and various mammals. The identification of host-Brucella interaction is crucial to understand host immunity against Brucella infection and Brucella pathogenesis against host immune responses. Most of the information about the inter-species interactions between host and Brucella genes is only available in the text of the scientific publications. Many text-mining systems for extracting gene and protein interactions have been proposed. However, only a few of them have been designed by considering the peculiarities of host-pathogen interactions. In this paper, we used a text mining approach for extracting host-Brucella gene-gene interactions from the abstracts of articles in PubMed. The gene-gene interactions here represent the interactions between genes and/or gene products (e.g., proteins). The SciMiner tool, originally designed for detecting mammalian gene/protein names in text, was extended to identify host and Brucella gene/protein names in the abstracts. Next, sentence-level and abstract-level co-occurrence based approaches, as well as sentence-level machine learning based methods, originally designed for extracting intra-species gene interactions, were utilized to extract the interactions among the identified host and Brucella genes. The extracted interactions were manually evaluated. A total of 46 host-Brucella gene interactions were identified and represented as an interaction network. Twenty four of these interactions were identified from sentence-level processing. Twenty two additional interactions were identified when abstract-level processing was performed. The Interaction Network Ontology (INO) was used to represent the identified interaction types at a hierarchical ontology structure. Ontological modeling of specific gene-gene interactions demonstrates that host-pathogen gene-gene interactions occur at experimental conditions which can be ontologically represented. Our

  19. Prediction and analysis of retinoblastoma related genes through gene ontology and KEGG.

    Science.gov (United States)

    Li, Zhen; Li, Bi-Qing; Jiang, Min; Chen, Lei; Zhang, Jian; Liu, Lin; Huang, Tao

    2013-01-01

    One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

  20. Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2013-01-01

    Full Text Available One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR method followed by incremental feature selection (IFS. 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

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

    Science.gov (United States)

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

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

  2. The Domain Shared by Computational and Digital Ontology: A Phenomenological Exploration and Analysis

    Science.gov (United States)

    Compton, Bradley Wendell

    2009-01-01

    The purpose of this dissertation is to explore and analyze a domain of research thought to be shared by two areas of philosophy: computational and digital ontology. Computational ontology is philosophy used to develop information systems also called computational ontologies. Digital ontology is philosophy dealing with our understanding of Being…

  3. Primer on Ontologies.

    Science.gov (United States)

    Hastings, Janna

    2017-01-01

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

  4. Globaltest and GOEAST: two different approaches for Gene Ontology analysis

    NARCIS (Netherlands)

    Hulsegge, B.; Kommadath, A.; Smits, M.A.

    2009-01-01

    Background Gene set analysis is a commonly used method for analysing microarray data by considering groups of functionally related genes instead of individual genes. Here we present the use of two gene set analysis approaches: Globaltest and GOEAST. Globaltest is a method for testing whether sets of

  5. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

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

  6. The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.

    Directory of Open Access Journals (Sweden)

    Mélanie Courtot

    Full Text Available BACKGROUND: When increased rates of adverse events following immunization are detected, regulatory action can be taken by public health agencies. However to be interpreted reports of adverse events must be encoded in a consistent way. Regulatory agencies rely on guidelines to help determine the diagnosis of the adverse events. Manual application of these guidelines is expensive, time consuming, and open to logical errors. Representing these guidelines in a format amenable to automated processing can make this process more efficient. METHODS AND FINDINGS: Using the Brighton anaphylaxis case definition, we show that existing clinical guidelines used as standards in pharmacovigilance can be logically encoded using a formal representation such as the Adverse Event Reporting Ontology we developed. We validated the classification of vaccine adverse event reports using the ontology against existing rule-based systems and a manually curated subset of the Vaccine Adverse Event Reporting System. However, we encountered a number of critical issues in the formulation and application of the clinical guidelines. We report these issues and the steps being taken to address them in current surveillance systems, and in the terminological standards in use. CONCLUSIONS: By standardizing and improving the reporting process, we were able to automate diagnosis confirmation. By allowing medical experts to prioritize reports such a system can accelerate the identification of adverse reactions to vaccines and the response of regulatory agencies. This approach of combining ontology and semantic technologies can be used to improve other areas of vaccine adverse event reports analysis and should inform both the design of clinical guidelines and how they are used in the future. AVAILABILITY: Sufficient material to reproduce our results is available, including documentation, ontology, code and datasets, at http://purl.obolibrary.org/obo/aero.

  7. Performing ontology.

    Science.gov (United States)

    Aspers, Patrik

    2015-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Robert Hoehndorf

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

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

    Science.gov (United States)

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

    2011-01-01

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

  10. Ontology-Based Platform for Conceptual Guided Dataset Analysis

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2016-05-31

    Nowadays organizations should handle a huge amount of both internal and external data from structured, semi-structured, and unstructured sources. This constitutes a major challenge (and also an opportunity) to current Business Intelligence solutions. The complexity and effort required to analyse such plethora of data implies considerable execution times. Besides, the large number of data analysis methods and techniques impede domain experts (laymen from an IT-assisted analytics perspective) to fully exploit their potential, while technology experts lack the business background to get the proper questions. In this work, we present a semantically-boosted platform for assisting layman users in (i) extracting a relevant subdataset from all the data, and (ii) selecting the data analysis technique(s) best suited for scrutinising that subdataset. The outcome is getting better answers in significantly less time. The platform has been evaluated in the music domain with promising results.

  11. The axiological ontology of occupational therapy: a philosophical analysis.

    Science.gov (United States)

    Drolet, Marie-Josée

    2014-01-01

    This article describes the results of a study analyzing several discourses on the values of occupational therapy and some philosophical assumptions upon which these values are based. A qualitative study of several values statements using the hermeneutical method--a conventional analytical approach in philosophy--was conducted. The literature review reveals that opinions on the values of occupational therapy differ greatly--no one value is shared among all the values statements examined. However, the majority of the texts mention occupational participation. A philosophical analysis of the literature shows that this value is based on a conception of human beings that can be traced back to the philosophical anthropologies of thinkers like Marx, Rousseau, Sartre, and Kant. The philosophical analysis also brought to light a certain conceptual confusion about what a value is. This article therefore offers some conceptual clarifications to help distinguish between values, beliefs, attitudes, principles, and non-evaluative concepts. It also presents the implications for practice of this philosophical analysis of values statements of the profession.

  12. An ontological knowledge based system for selection of process monitoring and analysis tools

    DEFF Research Database (Denmark)

    Singh, Ravendra; Gernaey, Krist; Gani, Rafiqul

    2010-01-01

    monitoring and analysis tools for a wide range of operations has made their selection a difficult, time consuming and challenging task. Therefore, an efficient and systematic knowledge base coupled with an inference system is necessary to support the optimal selection of process monitoring and analysis tools......, satisfying the process and user constraints. A knowledge base consisting of the process knowledge as well as knowledge on measurement methods and tools has been developed. An ontology has been designed for knowledge representation and management. The developed knowledge base has a dual feature. On the one...... procedures has been developed to retrieve the data/information stored in the knowledge base....

  13. Development of a Framework for Ontology Based Sentiment Analysis on Social Media

    Directory of Open Access Journals (Sweden)

    Kadir Tutar

    2015-10-01

    Full Text Available Developing internet technology, trend social media applications and web 2.0 have changed the internet usage habits of internet users. By this means the internet users have started to share their feelings and thoughts on social media from anywhere at anytime. With the increasement of social media usage, valuable feedback data has been increased more and more as well. To this end collection, interpretation and evaluation of this data has come into importance. 'Sentiment analysis' and 'natural language process' methods have been used on text-based data for evaluation and opinion mining to overcome this necessity. In this study, a new ontology-based sentiment analysis method has been developed in order to enhance the accuracy of results that obtained by current sentiment analysis methods. This newly developed method requires to model the domain-specific information on the ontology prior to the analysis procedure. Though this approach, more accurate and more qualified results have been provided to obtain in compared to classic sentiment analysis methods. Another important and innovative feature of this developed infrastructure is being able to do Turkish based sentiment analysis.

  14. Ontology-Based Gap Analysis for Technology Selection: A Knowledge Management Framework for the Support of Equipment Purchasing Processes

    Science.gov (United States)

    Macris, Aristomenis M.; Georgakellos, Dimitrios A.

    Technology selection decisions such as equipment purchasing and supplier selection are decisions of strategic importance to companies. The nature of these decisions usually is complex, unstructured and thus, difficult to be captured in a way that will be efficiently reusable. Knowledge reusability is of paramount importance since it enables users participate actively in process design/redesign activities stimulated by the changing technology selection environment. This paper addresses the technology selection problem through an ontology-based approach that captures and makes reusable the equipment purchasing process and assists in identifying (a) the specifications requested by the users' organization, (b) those offered by various candidate vendors' organizations and (c) in performing specifications gap analysis as a prerequisite for effective and efficient technology selection. This approach has practical appeal, operational simplicity, and the potential for both immediate and long-term strategic impact. An example from the iron and steel industry is also presented to illustrate the approach.

  15. Ontology-oriented MIS Domain Analysis Method%面向本体的MIS领域分析方法

    Institute of Scientific and Technical Information of China (English)

    房秀蓉; 李师贤

    2003-01-01

    Domain engineering is a reuse technology of large-grain size,it focuses the analysis,design and implementation within a specific domain. This paper focuses the first phase of domain engineermg,discusses a new approach of domain analysis-ontology-oriented MIS domain analysis method and introduces the implementation of the prototype system which supports this method.

  16. Domain-Specific Formal Ontology of Archaeology and Its Application in Knowledge Acquisition and Analysis

    Institute of Scientific and Technical Information of China (English)

    Chun-Xia Zhang; Cun-Gen Cao; Fang Gu; Jin-Xin Si

    2004-01-01

    Inherent heterogeneity and distribution of knowledge strongly prevent knowledge from sharing and reusing among different agents and software entities, and a formal ontology has been viewed as a promising means to tackle this problem. In this paper, a domain-specific formal ontology of archaeology is presented. The ontology mainly consists of three parts: archaeological categories, their relationships and axioms. The ontology not only captures the semantics of archaeological knowledge, but also provides archaeology with an explicit and formal specification of a shared conceptualization, thus making archaeological knowledge shareable and reusable across humans and machines in a structured fashion. Further, we propose a method to verify ontology correctness based on the individuals of categories. As applications of the ontology, we have developed an ontology-driven approach to knowledge acquisition from archaeological text and a question answering system for archaeological knowledge.

  17. Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis.

    Science.gov (United States)

    Pashaiasl, Maryam; Ebrahimi, Mansour; Ebrahimie, Esmaeil

    2016-09-01

    Diminished ovarian reserve (DOR) is one of the reasons for infertility that not only affects both older and young women. Ovarian reserve assessment can be used as a new prognostic tool for infertility treatment decision making. Here, up- and down-regulated gene expression profiles of granulosa cells were analysed to generate a putative interaction map of the involved genes. In addition, gene ontology (GO) analysis was used to get insight intol the biological processes and molecular functions of involved proteins in DOR. Eleven up-regulated genes and nine down-regulated genes were identified and assessed by constructing interaction networks based on their biological processes. PTGS2, CTGF, LHCGR, CITED, SOCS2, STAR and FSTL3 were the key nodes in the up-regulated networks, while the IGF2, AMH, GREM, and FOXC1 proteins were key in the down-regulated networks. MIRN101-1, MIRN153-1 and MIRN194-1 inhibited the expression of SOCS2, while CSH1 and BMP2 positively regulated IGF1 and IGF2. Ossification, ovarian follicle development, vasculogenesis, sequence-specific DNA binding transcription factor activity, and golgi apparatus are the major differential groups between up-regulated and down-regulated genes in DOR. Meta-analysis of publicly available transcriptomic data highlighted the high coexpression of CTGF, connective tissue growth factor, with the other key regulators of DOR. CTGF is involved in organ senescence and focal adhesion pathway according to GO analysis. These findings provide a comprehensive system biology based insight into the aetiology of DOR through network and gene ontology analyses.

  18. Engineering Ontologies

    OpenAIRE

    Borst, Pim; Akkermans, Hans; Top, Jan

    1997-01-01

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

  19. The neurological disease ontology.

    Science.gov (United States)

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

    2013-12-06

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

  20. Ontology-based content analysis of US patent applications from 2001-2010.

    Science.gov (United States)

    Weber, Lutz; Böhme, Timo; Irmer, Matthias

    2013-01-01

    Ontology-based semantic text analysis methods allow to automatically extract knowledge relationships and data from text documents. In this review, we have applied these technologies for the systematic analysis of pharmaceutical patents. Hierarchical concepts from the knowledge domains of chemical compounds, diseases and proteins were used to annotate full-text US patent applications that deal with pharmacological activities of chemical compounds and filed in the years 2001-2010. Compounds claimed in these applications have been classified into their respective compound classes to review the distribution of scaffold types or general compound classes such as natural products in a time-dependent manner. Similarly, the target proteins and claimed utility of the compounds have been classified and the most relevant were extracted. The method presented allows the discovery of the main areas of innovation as well as emerging fields of patenting activities - providing a broad statistical basis for competitor analysis and decision-making efforts.

  1. A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

    Science.gov (United States)

    Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

    2016-02-01

    Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Ontology-based analysis of multi-scale modeling of geographical features

    Institute of Scientific and Technical Information of China (English)

    WANG; Yanhui; LI; Xiaojuan; GONG; Huili

    2006-01-01

    As multi-scale databases based on scale series of map data are built, conceptual models are needed to define proper multi-scale representation formulas and to extract model entities and the relationships among them. However, the results of multi-scale conceptual abstraction schema may differ, according to which cognition, abstraction and application views are utilized, which presents an obvious obstacle to the reuse and sharing of spatial data. To facilitate the design of unified, common and objective abstract schema views for multi-scale spatial databases, this paper proposes an ontology-based analysis method for the multi-scale modeling of geographical features. It includes a three-layer ontology model, which serves as the framework for common multi-scale abstraction schema; an explanation of formulary abstractions accompanied by definitions of entities and their relationships at the same scale, as well as different scales,which are meant to provide strong feasibility, expansibility and speciality functions; and a case in point involving multi-scale representations of road features, to verify the method's feasibility.

  3. 基于知识本体的过程安全分析信息标准化%Standardized information for process hazard analysis based on ontology

    Institute of Scientific and Technical Information of China (English)

    吴重光; 许欣; 纳永良; 张卫华

    2012-01-01

    过程危险分析的主要目标是识别危险剧情.危险剧情能够表达团队“头脑风暴”安全评价过程也能表达评价结论.危险剧情的知识本体是标准化过程安全分析信息的准确描述.知识本体是概念表达的明确规范.依据设计知识本体所遵循的规则提出了一种过程安全分析信息标准化方法,称为剧情对象模型(scenario objectmodel,SOM).SOM能够表达安全分析信息的内容和结构,能够实施计算机自动推理和半定量计算.应用知识本体SOM有效实现了计算机辅助自动安全评价和安全信息的传递、复查和共享.%The principal objective of process hazard analysis is to identify hazard scenarios. Both the course of team brainstorming hazard evaluation and its result information can be expressed as hazard scenarios. Ontology of hazard scenarios is accurate expression of standardized process hazard analysis information. An ontology is an explicit specification of a conceptualization. According to design criteria for ontologies, a standardized process hazard analysis information called scenario object model (SOM) was proposed. SOM was used to represent contents and structures of hazard evaluation information. Computer automatic reasoning and semi-quantitative algorithms could be implemented on SOM. Computer-aided automatic hazard evaluation and transfer, auditing and sharing of safety information were realized effectively by using ontology SOM.

  4. Engineering Ontologies

    NARCIS (Netherlands)

    Borst, Pim; Akkermans, Hans; Top, Jan

    1997-01-01

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

  5. Ontology-based representation and analysis of host-Brucella interactions

    OpenAIRE

    Lin, Yu; Xiang, Zuoshuang; He, Yongqun

    2015-01-01

    Background Biomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer- and human-interpretable formats. Ontologies support data standardization and exchange and provide a basis for computer-assisted automated reasoning. IDOBRU is an ontology in the domain of Brucella and brucellosis. Brucella is a Gram-negative intracellular bacterium that causes brucellosis, the most common zoonotic disease in the world. In this stu...

  6. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

    Science.gov (United States)

    Koehler, Jacob; Rawlings, Chris; Verrier, Paul; Mitchell, Rowan; Skusa, Andre; Ruegg, Alexander; Philippi, Stephan

    2005-01-01

    The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

  7. OBIB-a novel ontology for biobanking.

    Science.gov (United States)

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

    2016-01-01

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

  8. Expression profiling and gene ontology analysis in fathead minnow (Pimephales promelas) liver following exposure to pulp and paper mill effluents

    Energy Technology Data Exchange (ETDEWEB)

    Costigan, Shannon L.; Werner, Julieta; Ouellet, Jacob D.; Hill, Lauren G. [Department of Biology, Lakehead University, 955 Oliver Road, Ontario P7B 5E1, (Canada); Law, R. David, E-mail: dlaw@lakeheadu.ca [Department of Biology, Lakehead University, 955 Oliver Road, Ontario P7B 5E1, (Canada)

    2012-10-15

    Many studies link pulp and paper mill effluent (PPME) exposure to adverse effects in fish populations present in the mill receiving environments. These impacts are often characteristic of endocrine disruption and may include impaired reproduction, development and survival. While these physiological endpoints are well-characterized, the molecular mechanisms causing them are not yet understood. To investigate changes in gene transcription induced by exposure to a PPME at several stages of treatment, male and female fathead minnows (FHMs) were exposed for 6 days to 25% (v/v) secondary (biologically) treated kraft effluent (TK) or 100% (v/v) combined mill outfall (CMO) from a mill producing both kraft pulp and newsprint. The gene expression changes in the livers of these fish were analyzed using a 22 K oligonucleotide microarray. Exposure to TK or CMO resulted in significant changes in the expression levels of 105 and 238 targets in male FHMs and 296 and 133 targets in females, respectively. Targets were then functionally analyzed using gene ontology tools to identify the biological processes in fish hepatocytes that were affected by exposure to PPME after its secondary treatment. Proteolysis was affected in female FHMs exposed to both TK and CMO. In male FHMs, no processes were affected by TK exposure, while sterol, isoprenoid, steroid and cholesterol biosynthesis and electron transport were up-regulated by CMO exposure. The results presented in this study indicate that short-term exposure to PPMEs affects the expression of reproduction-related genes in the livers of both male and female FHMs, and that secondary treatment of PPMEs may not neutralize all of their metabolic effects in fish. Gene ontology analysis of microarray data may enable identification of biological processes altered by toxicant exposure and thus provide an additional tool for monitoring the impact of PPMEs on fish populations.

  9. Statistical and Ontological Analysis of Adverse Events Associated with Monovalent and Combination Vaccines against Hepatitis A and B Diseases

    Science.gov (United States)

    Xie, Jiangan; Zhao, Lili; Zhou, Shangbo; He, Yongqun

    2016-01-01

    Vaccinations often induce various adverse events (AEs), and sometimes serious AEs (SAEs). While many vaccines are used in combination, the effects of vaccine-vaccine interactions (VVIs) on vaccine AEs are rarely studied. In this study, AE profiles induced by hepatitis A vaccine (Havrix), hepatitis B vaccine (Engerix-B), and hepatitis A and B combination vaccine (Twinrix) were studied using the VAERS data. From May 2001 to January 2015, VAERS recorded 941, 3,885, and 1,624 AE case reports where patients aged at least 18 years old were vaccinated with only Havrix, Engerix-B, and Twinrix, respectively. Using these data, our statistical analysis identified 46, 69, and 82 AEs significantly associated with Havrix, Engerix-B, and Twinrix, respectively. Based on the Ontology of Adverse Events (OAE) hierarchical classification, these AEs were enriched in the AEs related to behavioral and neurological conditions, immune system, and investigation results. Twenty-nine AEs were classified as SAEs and mainly related to immune conditions. Using a logistic regression model accompanied with MCMC sampling, 13 AEs (e.g., hepatosplenomegaly) were identified to result from VVI synergistic effects. Classifications of these 13 AEs using OAE and MedDRA hierarchies confirmed the advantages of the OAE-based method over MedDRA in AE term hierarchical analysis. PMID:27694888

  10. 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.

  11. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

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

  12. Bridging the gap between data acquisition and inference ontologies: toward ontology-based link discovery

    Science.gov (United States)

    Goldstein, Michel L.; Morris, Steven A.; Yen, Gary G.

    2003-09-01

    Bridging the gap between low level ontologies used for data acquisition and high level ontologies used for inference is essential to enable the discovery of high-level links between low-level entities. This is of utmost importance in many applications, where the semantic distance between the observable evidence and the target relations is large. Examples of these applications would be detection of terrorist activity, crime analysis, and technology monitoring, among others. Currently this inference gap has been filled by expert knowledge. However, with the increase of the data and system size, it has become too costly to perform such manual inference. This paper proposes a semi-automatic system to bridge the inference gap using network correlation methods, similar to Bayesian Belief Networks, combined with hierarchical clustering, to group and organize data so that experts can observe and build the inference gap ontologies quickly and efficiently, decreasing the cost of this labor-intensive process. A simple application of this method is shown here, where the co-author collaboration structure ontology is inferred from the analysis of a collection of journal publications on the subject of anthrax. This example uncovers a co-author collaboration structures (a well defined ontology) from a scientific publication dataset (also a well defined ontology). Nevertheless, the evidence of author collaboration is poorly defined, requiring the use of evidence from keywords, citations, publication dates, and paper co-authorship. The proposed system automatically suggests candidate collaboration group patterns for evaluation by experts. Using an intuitive graphic user interface, these experts identify, confirm and refine the proposed ontologies and add them to the ontology database to be used in subsequent processes.

  13. Efficient Management of Biomedical Ontology Versions

    Science.gov (United States)

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

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

  14. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

    Science.gov (United States)

    Kotera, Masaaki; Nishimura, Yosuke; Nakagawa, Zen-ichi; Muto, Ai; Moriya, Yuki; Okamoto, Shinobu; Kawashima, Shuichi; Katayama, Toshiaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2014-12-01

    Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

  15. Ontology Research

    OpenAIRE

    Welty, Christopher

    2003-01-01

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

  16. Ontology of the False State

    Directory of Open Access Journals (Sweden)

    Testa Italo

    2015-09-01

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

  17. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

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

  18. Generating Application Ontologies from Reference Ontologies

    OpenAIRE

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

    2008-01-01

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

  19. FYPO: the fission yeast phenotype ontology.

    Science.gov (United States)

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

    2013-07-01

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

  20. An analysis of fundamental concepts in the conceptual framework using ontology technologies

    CSIR Research Space (South Africa)

    Gerber, MC

    2014-01-01

    Full Text Available , which aim to address the problems of vagueness, inconsistency and ambiguity. This paper reports on the findings of a design science research (DSR) project that, as artefact, developed a first version ontology-based formal language representing...

  1. Role of Ontology in Information Retrieval

    Institute of Scientific and Technical Information of China (English)

    WU Dan; WANG Hui-lin

    2006-01-01

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

  2. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

    Directory of Open Access Journals (Sweden)

    Ramina Angelo

    2008-07-01

    Full Text Available Abstract Background After 10-year-use of AFLP (Amplified Fragment Length Polymorphism technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO, consisting in three structured vocabularies (i.e. ontologies describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization

  3. DESIGN AND IMPLEMENTATION OF ONTOLOGY BASED ON SEMANTIC ANALYSIS FOR GIS APPLICATION

    Directory of Open Access Journals (Sweden)

    S.S Mantha

    2011-09-01

    Full Text Available The Agricultural Census information is a leading source of facts and figures about a country’s agricultural development. Such information is used by many who provide services to farmers and rural communities including federal, state and local governments, agribusinesses etc. Also such information when integrated with other agricultural surveys and statistics can help in monitoring progress towards the achievement of Millennium Development Goals (MDGs of a country. But such huge volumes of census data are available at various geo-spatial portals either in proprietary formats like shape files, .dat files etc or in form of database tables, word documents, PDF’s etc. In order to do analysis or to just see the progress of a particular area such huge datasheets have to be scanned. This paper provides solutions to various problems related to Geo-spatial Agricultural Census data in three aspects: (1 Storage / Organization of census data using enhanced methods such as ontologies. (2 Visualization of data using Google Maps and Column Charts. (3 Analysis of data using interactive methods like Column Charts.

  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. Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.

    Science.gov (United States)

    Malhotra, Ashutosh; Gündel, Michaela; Rajput, Abdul Mateen; Mevissen, Heinz-Theodor; Saiz, Albert; Pastor, Xavier; Lozano-Rubi, Raimundo; Martinez-Lapiscina, Elena H; Martinez-Lapsicina, Elena H; Zubizarreta, Irati; Mueller, Bernd; Kotelnikova, Ekaterina; Toldo, Luca; Hofmann-Apitius, Martin; Villoslada, Pablo

    2015-01-01

    In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology. Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports. The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information.

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

    Science.gov (United States)

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

    2014-01-01

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

  7. Rice Transcriptome Analysis to Identify Possible Herbicide Quinclorac Detoxification Genes

    Directory of Open Access Journals (Sweden)

    Wenying eXu

    2015-09-01

    Full Text Available Quinclorac is a highly selective auxin-type herbicide, and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world’s rice yield. The herbicide mode of action of quinclorac has been proposed and hormone interactions affect quinclorac signaling. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and environmental health problems.In this study, we used 57K Affymetrix rice whole-genome array to identify quinclorac signaling response genes to study the molecular mechanisms of action and detoxification of quinclorac in rice plants. Overall, 637 probe sets were identified with differential expression levels under either 6 or 24 h of quinclorac treatment. Auxin-related genes such as GH3 and OsIAAs responded to quinclorac treatment. Gene Ontology analysis showed that genes of detoxification-related family genes were significantly enriched, including cytochrome P450, GST, UGT, and ABC and drug transporter genes. Moreover, real-time RT-PCR analysis showed that top candidate P450 families such as CYP81, CYP709C and CYP72A genes were universally induced by different herbicides. Some Arabidopsis genes for the same P450 family were up-regulated under quinclorac treatment.We conduct rice whole-genome GeneChip analysis and the first global identification of quinclorac response genes. This work may provide potential markers for detoxification of quinclorac and biomonitors of environmental chemical pollution.

  8. Ontology Localization

    OpenAIRE

    2009-01-01

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

  9. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  11. OAE: The Ontology of Adverse Events.

    Science.gov (United States)

    He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry

    2014-01-01

    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term 'adverse event' denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. For example, using the data extracted from the Vaccine Adverse Event Reporting System (VAERS), OAE was used to analyse vaccine adverse events associated with the administrations of different types of influenza vaccines. OAE has also been used to represent and classify the vaccine adverse events cited in package inserts of FDA-licensed human vaccines in the USA. OAE is a biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e

  12. Improvements to cardiovascular gene ontology.

    Science.gov (United States)

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

    2009-07-01

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

  13. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

    Science.gov (United States)

    Wei, Qing; Khan, Ishita K; Ding, Ziyun; Yerneni, Satwica; Kihara, Daisuke

    2017-03-20

    The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions. We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .

  14. Aplicación de visualización de una ontología para el dominio del análisis del semen humano Application to visualize an ontology for the human semen analysis domain

    Directory of Open Access Journals (Sweden)

    Roberto Casañas

    2007-06-01

    Full Text Available En este trabajo se presenta el diseño e implementación de una ontología para el dominio del análisis del semen humano, cuyo objetivo es representar, organizar, formalizar y estandarizar el conocimiento del dominio, para que éste pueda ser compartido y reutilizado por distintos grupos de personas y aplicaciones de software. Para visualizar la ontología se desarrolló una aplicación basada en una arquitectura cliente/servidor para ambientes Web, la cual está constituida por un módulo de Administración y otro de Acceso Público. A través del primero se mantiene el sitio Web de la ontología, mientras que el segundo permite a los usuarios acceder al conocimiento almacenado y a un conjunto de recursos tales como imágenes, videos, artículos relativos al dominio, manuales y protocolos de laboratorio. La arquitectura propuesta facilita la observación y recuperación de las complejas estructuras de conocimiento, así como la navegación y administración de la información representada en la ontología. El enfoque utilizado en el diseño de los mecanismos de recuperación de información está dirigido tanto a usuarios poco familiarizados con el vocabulario del dominio, como a aquellos que ya lo conocen. Esta funcionalidad es de especial interés dado lo heterogénea que resulta la audiencia a la que está dirigida la ontología, como son profesionales y estudiantes de las ciencias de la salud, entre otros. La metodología Methontology fue seleccionada para desarrollar la ontología y se utilizó el editor Protégé para su implementación.The following work presents the design and implementation of an ontology for human semen analysis whose objective is to present, organize, formalize and standardize the domain knowledge, in order to be shared and reused by different groups of people and software applications. To visualize this ontology, a Web application based on a client/server architecture was developed, which is constituted by an

  15. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

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

  16. Domain-Specific Ontology of Botany

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  17. Analysis of Deviations in an Agent and Ontology-Based Dialogue Management System

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Algorithms of detecting dialogue deviations from a dialogue topic in an agent and ontology-based dialogue management system(AODMS) are proposed. In AODMS, agents and ontologies are introduced to represent domain knowledge. And general algorithms that model dialogue phenomena in different domains can be realized in that complex relationships between knowledge in different domains can be described by ontologies. An evaluation of the dialogue management system with deviation-judging algorithms on 736 utterances shows that the AODMS is able to talk about the given topic consistently and answer 86.6% of the utterances, while only 72.1% of the utterances can be responded correctly without deviation-judging module.

  18. Ontology-based meta-analysis of global collections of high-throughput public data.

    Directory of Open Access Journals (Sweden)

    Ilya Kupershmidt

    Full Text Available BACKGROUND: The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today. METHODOLOGY/RESULTS: We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets. CONCLUSIONS: Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis.

  19. Visualization of mappings between the gene ontology and cluster trees

    Science.gov (United States)

    Jusufi, Ilir; Kerren, Andreas; Aleksakhin, Vladyslav; Schreiber, Falk

    2012-01-01

    Ontologies and hierarchical clustering are both important tools in biology and medicine to study high-throughput data such as transcriptomics and metabolomics data. Enrichment of ontology terms in the data is used to identify statistically overrepresented ontology terms, giving insight into relevant biological processes or functional modules. Hierarchical clustering is a standard method to analyze and visualize data to find relatively homogeneous clusters of experimental data points. Both methods support the analysis of the same data set, but are usually considered independently. However, often a combined view is desired: visualizing a large data set in the context of an ontology under consideration of a clustering of the data. This paper proposes a new visualization method for this task.

  20. The use of Gene Ontology terms and KEGG pathways for analysis and prediction of oncogenes.

    Science.gov (United States)

    Xing, Zhihao; Chu, Chen; Chen, Lei; Kong, Xiangyin

    2016-11-01

    Oncogenes are a type of genes that have the potential to cause cancer. Most normal cells undergo programmed cell death, namely apoptosis, but activated oncogenes can help cells avoid apoptosis and survive. Thus, studying oncogenes is helpful for obtaining a good understanding of the formation and development of various types of cancers. In this study, we proposed a computational method, called OPM, for investigating oncogenes from the view of Gene Ontology (GO) and biological pathways. All investigated genes, including validated oncogenes retrieved from some public databases and other genes that have not been reported to be oncogenes thus far, were encoded into numeric vectors according to the enrichment theory of GO terms and KEGG pathways. Some popular feature selection methods, minimum redundancy maximum relevance and incremental feature selection, and an advanced machine learning algorithm, random forest, were adopted to analyze the numeric vectors to extract key GO terms and KEGG pathways. Along with the oncogenes, GO terms and KEGG pathways were discussed in terms of their relevance in this study. Some important GO terms and KEGG pathways were extracted using feature selection methods and were confirmed to be highly related to oncogenes. Additionally, the importance of these terms and pathways in predicting oncogenes was further demonstrated by finding new putative oncogenes based on them. This study investigated oncogenes based on GO terms and KEGG pathways. Some important GO terms and KEGG pathways were confirmed to be highly related to oncogenes. We hope that these GO terms and KEGG pathways can provide new insight for the study of oncogenes, particularly for building more effective prediction models to identify novel oncogenes. The program is available upon request. We hope that the new findings listed in this study may provide a new insight for the investigation of oncogenes. This article is part of a Special Issue entitled "System Genetics" Guest Editor

  1. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.

    Science.gov (United States)

    Chen, Lei; Zhang, Yu-Hang; Wang, ShaoPeng; Zhang, YunHua; Huang, Tao; Cai, Yu-Dong

    2017-01-01

    Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.

  2. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    Science.gov (United States)

    Vashisht, Shikha; Bagler, Ganesh

    2012-01-01

    Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  3. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    Directory of Open Access Journals (Sweden)

    Shikha Vashisht

    Full Text Available Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  4. Ontology Requirements Specification

    OpenAIRE

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

    2012-01-01

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

  5. Semi-automated ontology generation and evolution

    Science.gov (United States)

    Stirtzinger, Anthony P.; Anken, Craig S.

    2009-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Rong Gui

    2016-08-01

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

  7. An Analysis of the Ontological Causal Relation in Physics and Its Educational Implications

    Science.gov (United States)

    Cheong, Yong Wook

    2016-01-01

    An ontological causal relation is a quantified relation between certain interactions and changes in corresponding properties. Key ideas in physics, such as Newton's second law and the first law of thermodynamics, are representative examples of these relations. In connection with the teaching and learning of these relations, this study investigated…

  8. An Analysis of the Ontological Causal Relation in Physics and Its Educational Implications

    Science.gov (United States)

    Cheong, Yong Wook

    2016-01-01

    An ontological causal relation is a quantified relation between certain interactions and changes in corresponding properties. Key ideas in physics, such as Newton's second law and the first law of thermodynamics, are representative examples of these relations. In connection with the teaching and learning of these relations, this study investigated…

  9. Ontological backdrop

    DEFF Research Database (Denmark)

    Galle, Per

    2000-01-01

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

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

    Science.gov (United States)

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

    2013-10-08

    Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases. We created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data with perfect

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

    Science.gov (United States)

    Shi, Wei; Wang, Hongwei; He, Shaoyi

    2013-12-01

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

  12. Impact of ontology evolution on functional analyses.

    Science.gov (United States)

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

    2012-10-15

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

  13. Exploration of very high spatial resolution data for vegetation mapping using cartographic ontologies: Identifying life forms to mapping formations

    Science.gov (United States)

    Rodriguez-Gallegos, Hugo Benigno

    Vegetation mapping is often considered the process of identifying landscape patterns of individuals or clusters of species or life forms (LF). At the landscape scale, the larger pattern represented by individuals or clusters represents the conceptualization of "vegetation mapping" and can be used as a building block to describe an ecosystem. To represent these building blocks or LF a "common entity (CE)" concept is introduced to represent the components of Formations as described by the National Vegetation Classification (NVC) system. The NVC has established protocols to consistently represent plant communities and promote coordinated management, particularly across jurisdictional boundaries. However, it is not a universal standard and the methods of producing detailed maps of vegetation CE from very high spatial resolution (VHR) remote sensing data are important research questions. This research addressed how best to understand and represent plant cover in arid regions, the most effective methods of mapping vegetation cover using high spatial resolution data, how to assess the accuracy of these maps, and their value in establishing more standardized mapping protocols across ecosystems. Utilizing VHR products from the IKONOS and QuickBird sensors the study focused on the Coronado National Memorial and Chiricahua National Monument in Arizona and Los Ajos and Pinacate - Grand Desierto Biosphere Reserves in Mexico. Individual CE were semi-automatically mapped incorporating spectral, textural and geostatistical variables. The results were evaluated across sensors, study sites, and input variables. In addition, multiple methods of acquiring field data for accuracy assessment were evaluated and then an evaluation was made of a semi-automatic determination of Formation based on CE. The results of the study suggest consistency across study sites using the IKONOS data. A comparison between VHR products from the same place is feasible but sensor spectral differences may

  14. Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

    Directory of Open Access Journals (Sweden)

    Kim Nora

    2012-07-01

    Full Text Available Abstract Background It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO. Results We first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs. Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, ‘Regulation of Cellular Component Organization and Biogenesis’, a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, ‘Actin Cytoskeleton’, a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively. Conclusions Pathway

  15. 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.

  16. 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...

  17. Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

    Science.gov (United States)

    Christen, Victor; Hartung, Michael; Groß, Anika

    2015-01-01

    A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

  18. HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

    Science.gov (United States)

    Deng, Yue; Gao, Lin; Wang, Bingbo; Guo, Xingli

    2015-01-01

    Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO. HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).

  19. Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO.

    Directory of Open Access Journals (Sweden)

    Uma D Vempati

    Full Text Available Huge amounts of high-throughput screening (HTS data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO. BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

  20. Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).

    Science.gov (United States)

    Vempati, Uma D; Przydzial, Magdalena J; Chung, Caty; Abeyruwan, Saminda; Mir, Ahsan; Sakurai, Kunie; Visser, Ubbo; Lemmon, Vance P; Schürer, Stephan C

    2012-01-01

    Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

  1. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

    Science.gov (United States)

    Mi, Huaiyu; Huang, Xiaosong; Muruganujan, Anushya; Tang, Haiming; Mills, Caitlin; Kang, Diane; Thomas, Paul D

    2017-01-04

    The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new 'hierarchical view' of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution.

  2. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

    Science.gov (United States)

    Mi, Huaiyu; Huang, Xiaosong; Muruganujan, Anushya; Tang, Haiming; Mills, Caitlin; Kang, Diane; Thomas, Paul D.

    2017-01-01

    The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new ‘hierarchical view’ of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution. PMID:27899595

  3. 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.

  4. Gene Ontology Consortium: going forward

    Science.gov (United States)

    2015-01-01

    The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. PMID:25428369

  5. Generating application ontologies from reference ontologies.

    Science.gov (United States)

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

    2008-11-06

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

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

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

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

  7. Building a biomedical ontology recommender web service.

    Science.gov (United States)

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

    2010-06-22

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

  8. Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

    Science.gov (United States)

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

    2014-10-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

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

    LENUS (Irish Health Repository)

    Anney, Richard J L

    2012-02-01

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

  10. 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

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F

    2012-03-01

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

  13. DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

    Science.gov (United States)

    Mazandu, Gaston K; Mulder, Nicola J

    2013-09-25

    The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.

  14. The Orthology Ontology: development and applications.

    Science.gov (United States)

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

    2016-06-04

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

  15. The language of gene ontology: a Zipf’s law analysis

    Directory of Open Access Journals (Sweden)

    Kalankesh Leila

    2012-06-01

    Full Text Available Abstract Background Most major genome projects and sequence databases provide a GO annotation of their data, either automatically or through human annotators, creating a large corpus of data written in the language of GO. Texts written in natural language show a statistical power law behaviour, Zipf’s law, the exponent of which can provide useful information on the nature of the language being used. We have therefore explored the hypothesis that collections of GO annotations will show similar statistical behaviours to natural language. Results Annotations from the Gene Ontology Annotation project were found to follow Zipf’s law. Surprisingly, the measured power law exponents were consistently different between annotation captured using the three GO sub-ontologies in the corpora (function, process and component. On filtering the corpora using GO evidence codes we found that the value of the measured power law exponent responded in a predictable way as a function of the evidence codes used to support the annotation. Conclusions Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that provide a signal which correlates with the nature of the evidence codes used to support the annotations, suggesting that the measured exponent might provide a signal regarding the information content of the annotation.

  16. Visualization and analysis of microarray and gene ontology data with treemaps

    Directory of Open Access Journals (Sweden)

    Babaria Ketan

    2004-06-01

    Full Text Available Abstract Background The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access. Results Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform. Conclusions Treemaps allow users to view and query the data from an experiment on a single computer monitor screen. Treemap 4.0 can be used to visualize various genome data, and is particularly useful for revealing patterns and details within complex data sets.

  17. Orymold: ontology based gene expression data integration and analysis tool applied to rice

    Directory of Open Access Journals (Sweden)

    Segura Jordi

    2009-05-01

    Full Text Available Abstract Background Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A widely accepted approach to solve these issues has been the creation and use of controlled vocabularies (ontologies. Ontologies allow for the formalization of domain knowledge, which in turn enables generalization in the creation of querying interfaces as well as in the integration of heterogeneous data, providing both human and machine readable interfaces. Results We designed and implemented a software tool that allows investigators to create their own semantic model of an organism and to use it to dynamically integrate expression data obtained from DNA microarrays and other probe based technologies. The software provides tools to use the semantic model to postulate and validate of hypotheses on the spatial and temporal expression and function of genes. In order to illustrate the software's use and features, we used it to build a semantic model of rice (Oryza sativa and integrated experimental data into it. Conclusion In this paper we describe the development and features of a flexible software application for dynamic gene expression data annotation, integration, and exploration called Orymold. Orymold is freely available for non-commercial users from http://www.oryzon.com/media/orymold.html

  18. 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.

  19. How the gene ontology evolves.

    Science.gov (United States)

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

    2011-08-05

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

  20. Simple Ontology Format (SOFT)

    Energy Technology Data Exchange (ETDEWEB)

    2011-10-01

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

  1. Extending the Interpretation of Gene Profiling Microarray Experiments to Pathway Analysis Through the Use of Gene Ontology Terms

    Science.gov (United States)

    Chatziioannou, Aristotelis; Moulos, Panagiotis

    Microarray technology allows the survey of gene expression at a global level by measuring mRNA abundance. However, the grand complexity characterizing a microarray experiment entails the development of computationally powerful tools apt for probing the biological problem studied. Here we propose a suite for flexible, adaptable to a wide range of possible needs of the biological end-user, data-driven interpretation of microarray experiments. The suite is implemented in MATLAB and is making use of two modules, able to perform all steps of typical microarray data analysis starting from data standardization and normalization up to statistical selection and pathway analysis utilizing Gene Ontology Term annotations for the species genomes interrogated, whereas due to its modular structure it is scalable thus enabling the incorporation or its seamless assembly with other existing tools.

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

    Science.gov (United States)

    Jupp, Simon; Stevens, Robert; Hoehndorf, Robert

    2012-04-24

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

  3. Factor analysis identifies subgroups of constipation

    Institute of Scientific and Technical Information of China (English)

    Philip G Dinning; Mike Jones; Linda Hunt; Sergio E Fuentealba; Jamshid Kalanter; Denis W King; David Z Lubowski; Nicholas J Talley; Ian J Cook

    2011-01-01

    AIM: To determine whether distinct symptom groupings exist in a constipated population and whether such grouping might correlate with quantifiable pathophysiological measures of colonic dysfunction. METHODS: One hundred and ninety-one patients presenting to a Gastroenterology clinic with constipation and 32 constipated patients responding to a newspaper advertisement completed a 53-item, wide-ranging selfreport questionnaire. One hundred of these patients had colonic transit measured scintigraphically. Factor analysis determined whether constipation-related symptoms grouped into distinct aspects of symptomatology. Cluster analysis was used to determine whether individual patients naturally group into distinct subtypes. RESULTS: Cluster analysis yielded a 4 cluster solution with the presence or absence of pain and laxative unresponsiveness providing the main descriptors. Amongst all clusters there was a considerable proportion of patients with demonstrable delayed colon transit, irritable bowel syndrome positive criteria and regular stool frequency. The majority of patients with these characteristics also reported regular laxative use. CONCLUSION: Factor analysis identified four constipation subgroups, based on severity and laxative unresponsiveness, in a constipated population. However, clear stratification into clinically identifiable groups remains imprecise.

  4. Identifying marker typing incompatibilities in linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Stringham, H.M.; Boehnke, M. [Univ. of Michigan, Ann Arbor, MI (United States)

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  5. Datamining with Ontologies.

    Science.gov (United States)

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

    2016-01-01

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

  6. Assessing HTS performance using BioAssay Ontology: screening and analysis of a bacterial phospho-N-acetylmuramoyl-pentapeptide translocase campaign.

    Science.gov (United States)

    Moberg, Andreas; Zander Balderud, Linda; Hansson, Eva; Boyd, Helen

    2014-01-01

    With the public availability of biochemical assays and screening data constantly increasing, new applications for data mining and method analysis are evolving in parallel. One example is BioAssay Ontology (BAO) for systematic classification of assays based on screening setup and metadata annotations. In this article we report a high-throughput screening (HTS) against phospho-N-acetylmuramoyl-pentapeptide translocase (MraY), an attractive antibacterial drug target involved in peptidoglycan synthesis. The screen resulted in novel chemistry identification using a fluorescence resonance energy transfer assay. To address a subset of the false positive hits, a frequent hitter analysis was performed using an approach in which MraY hits were compared with hits from similar assays, previously used for HTS. The MraY assay was annotated according to BAO and three internal reference assays, using a similar assay design and detection technology, were identified. Analyzing the assays retrospectively, it was clear that both MraY and the three reference assays all showed a high false positive rate in the primary HTS assays. In the case of MraY, false positives were efficiently identified by applying a method to correct for compound interference at the hit-confirmation stage. Frequent hitter analysis based on the three reference assays with similar assay method identified additional false actives in the primary MraY assay as frequent hitters. This article demonstrates how assays annotated using BAO terms can be used to identify closely related reference assays, and that analysis based on these assays clearly can provide useful data to influence assay design, technology, and screening strategy.

  7. Logical Development of the Cell Ontology

    Directory of Open Access Journals (Sweden)

    Blake Judith A

    2011-01-01

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

  8. Invariance as a Tool for Ontology of Information

    Directory of Open Access Journals (Sweden)

    Marcin J. Schroeder

    2016-03-01

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

  9. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

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

  10. Gene ontology study of methyl jasmonate-treated and non-treated hairy roots of Panax ginseng to identify genes involved in secondary metabolic pathway.

    Science.gov (United States)

    Sathiyamoorthy, S; In, J G; Gayathri, S; Kim, Y Ju; Yang, D Ch

    2010-07-01

    The roots of Panax ginseng C.A. Meyer, known as Korean ginseng have been a valuable and important folk medicine in East Asian countries. It mainly used to maintain the homeostasis of the human body, with the presence ofginsenosides and non-saponin compounds like phenol compounds, acidic polysaccharides and polyethylene compounds. Functional genomics aid to annotate based on gene ontology. In this study, we focused on the genes involving in secondary metabolic pathways and to visualize temporal changes of gene expression in ginseng hairy roots with methyl ester methyl jasmonate (MeJA) along with non-treated hairy roots. A 5.774 EST clones were clustered and assembled as 501 contigs and 2.955 singletons. Annotations categorized with molecular functions, biological processes, cellular compounds of gene ontological terms and biochemical functions, enzyme commission to sequences were assigned to metabolic pathways of Kyoto Encyclopedia of Genes and Genomes database. Comparatively, EST sequences are assigned to cellular process, metabolic process, biotic and abiotic stress stimuli, developmental and biological regulations and transports are up-regulated 2-3 fold in MeJA treated hairy roots. 46 different sub groups of enzymes found in the MeJA treated plants. These annotated ESTs represents a significant proportion of the P. ginseng and provides molecular resource for developmental of microarrays for gene expression studies concerning development, metabolism and reproduction.

  11. Contributions to an animal trait ontology.

    Science.gov (United States)

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

    2012-06-01

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

  12. The Human Phenotype Ontology in 2017

    Science.gov (United States)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie; Aymé, Ségolène; Baynam, Gareth; Bello, Susan M.; Boerkoel, Cornelius F.; Boycott, Kym M.; Brudno, Michael; Buske, Orion J.; Chinnery, Patrick F.; Cipriani, Valentina; Connell, Laureen E.; Dawkins, Hugh J.S.; DeMare, Laura E.; Devereau, Andrew D.; de Vries, Bert B.A.; Firth, Helen V.; Freson, Kathleen; Greene, Daniel; Hamosh, Ada; Helbig, Ingo; Hum, Courtney; Jähn, Johanna A.; James, Roger; Krause, Roland; F. Laulederkind, Stanley J.; Lochmüller, Hanns; Lyon, Gholson J.; Ogishima, Soichi; Olry, Annie; Ouwehand, Willem H.; Pontikos, Nikolas; Rath, Ana; Schaefer, Franz; Scott, Richard H.; Segal, Michael; Sergouniotis, Panagiotis I.; Sever, Richard; Smith, Cynthia L.; Straub, Volker; Thompson, Rachel; Turner, Catherine; Turro, Ernest; Veltman, Marijcke W.M.; Vulliamy, Tom; Yu, Jing; von Ziegenweidt, Julie; Zankl, Andreas; Züchner, Stephan; Zemojtel, Tomasz; Jacobsen, Julius O.B.; Groza, Tudor; Smedley, Damian; Mungall, Christopher J.; Haendel, Melissa; Robinson, Peter N.

    2017-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology. PMID:27899602

  13. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

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

  14. Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis.

    Science.gov (United States)

    Zhang, Yijuan; Akintola, Oluwafemi S; Liu, Ken J A; Sun, Bingyun

    2016-01-10

    Microarray (MA) and high-throughput sequencing are two commonly used detection systems for global gene expression profiling. Although these two systems are frequently used in parallel, the differences in their final results have not been examined thoroughly. Transcriptomic analysis of housekeeping (HK) genes provides a unique opportunity to reliably examine the technical difference between these two systems. We investigated here the structure, genome location, expression quantity, microarray probe coverage, as well as biological functions of differentially identified human HK genes by 9 MA and 6 sequencing studies. These in-depth analyses allowed us to discover, for the first time, a subset of transcripts encoding membrane, cell surface and nuclear proteins that were prone to differential identification by the two platforms. We hope that the discovery can aid the future development of these technologies for comprehensive transcriptomic studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.

    Science.gov (United States)

    Koç, Ibrahim; Caetano-Anollés, Gustavo

    2017-01-01

    The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.

  16. Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data

    Science.gov (United States)

    Jiang, Bing; Li, Shuwen; Jiang, Zhi

    2017-01-01

    Gastric cancer is one of the most severe complex diseases with high morbidity and mortality in the world. The molecular mechanisms and risk factors for this disease are still not clear since the cancer heterogeneity caused by different genetic and environmental factors. With more and more expression data accumulated nowadays, we can perform integrative analysis for these data to understand the complexity of gastric cancer and to identify consensus players for the heterogeneous cancer. In the present work, we screened the published gene expression data and analyzed them with integrative tool, combined with pathway and gene ontology enrichment investigation. We identified several consensus differentially expressed genes and these genes were further confirmed with literature mining; at last, two genes, that is, immunoglobulin J chain and C-X-C motif chemokine ligand 17, were screened as novel gastric cancer associated genes. Experimental validation is proposed to further confirm this finding. PMID:28232943

  17. One Song, Many Works: A Pluralist Ontology of Rock

    Directory of Open Access Journals (Sweden)

    Dan Burkett

    2016-01-01

    Full Text Available A number of attempts have been made to construct a plausible ontology of rock music. Each of these ontologies identifies a single type of ontological entity as the “work” in rock music. Yet, all the suggestions advanced to date fail to capture some important considerations about how we engage with music of this tradition. This prompted Lee Brown to advocate a healthy skepticism of higher-order musical ontologies. I argue here that we should instead embrace a pluralist ontology of rock, an ontology that recognizes more than one kind of entity as “the work” in rock music. I contend that this approach has a number of advantages over other ontologies of rock, including that of allowing us to make some comparisons across ontological kinds.

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

    Science.gov (United States)

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

    2017-03-23

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

  19. Análisis de terminologías de salud para su utilización como ontologías computacionales en los sistemas de información clínicos Analysis of health terminologies for use as ontologies in healthcare information systems

    Directory of Open Access Journals (Sweden)

    Maria Teresa Romá-Ferri

    2008-10-01

    limitations imposed by standardized terms. The objective of this study was to establish the extent to which terminologies could be used for the design of ontologies, which could be serve as an aid to resolve problems such as semantic interoperability and knowledge reusability in healthcare information systems. Methods: To determine the extent to which terminologies could be used as ontologies, six of the most important terminologies in clinical, epidemiologic, documentation and administrative-economic contexts were analyzed. The following characteristics were verified: conceptual coverage, hierarchical structure, conceptual granularity of the categories, conceptual relations, and the language used for conceptual representation. Results: MeSH, DeCS and UMLS ontologies were considered lightweight. The main differences among these ontologies concern conceptual specification, the types of relation and the restrictions among the associated concepts. SNOMED and GALEN ontologies have declaratory formalism, based on logical descriptions. These ontologies include explicit qualities and show greater restrictions among associated concepts and rule combinations and were consequently considered as heavyweight. Conclusions: Analysis of the declared representation of the terminologies shows the extent to which they could be reused as ontologies. Their degree of usability depends on whether the aim is for healthcare information systems to solve problems of semantic interoperability (lightweight ontologies or to reuse the systems' knowledge as an aid to decision making (heavyweight ontologies and for non-structured information retrieval, extraction, and classification.

  20. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

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

  1. Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry.

    Science.gov (United States)

    Kumar, Ravindra; Samal, Sabindra K; Routray, Samapika; Dash, Rupesh; Dixit, Anshuman

    2017-05-30

    In the recent years, bioinformatics methods have been reported with a high degree of success for candidate gene identification. In this milieu, we have used an integrated bioinformatics approach assimilating information from gene ontologies (GO), protein-protein interaction (PPI) and network analysis to predict candidate genes related to oral squamous cell carcinoma (OSCC). A total of 40973 PPIs were considered for 4704 cancer-related genes to construct human cancer gene network (HCGN). The importance of each node was measured in HCGN by ten different centrality measures. We have shown that the top ranking genes are related to a significantly higher number of diseases as compared to other genes in HCGN. A total of 39 candidate oral cancer target genes were predicted by combining top ranked genes and the genes corresponding to significantly enriched oral cancer related GO terms. Initial verification using literature and available experimental data indicated that 29 genes were related with OSCC. A detailed pathway analysis led us to propose a role for the selected candidate genes in the invasion and metastasis in OSCC. We further validated our predictions using immunohistochemistry (IHC) and found that the gene FLNA was upregulated while the genes ARRB1 and HTT were downregulated in the OSCC tissue samples.

  2. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

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

  3. A Posteriori Ontology Engineering for Data-Driven Science

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-05-28

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

  4. 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 leadinginformaticians, biologists, clinicians, and ontologists funded by the NIHRoadmap to develop innovative technology and methods that allowscientists to record, manage, and disseminate biomedical information andknowledge in machine-processable form. The goals of the Center are: (1)to help unify the divergent and isolated efforts in ontology developmentby promoting high quality open-source, standards-based tools to create,manage, and use ontologies, (2) to create new software tools so thatscientists 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 toolsand 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 thebiomedical community. The Center is working toward these objectives byproviding tools to develop ontologies and to annotate experimental data,and by developing resources to integrate and relate existing ontologiesas well as by creating repositories of biomedical data that are annotatedusing those ontologies. The Center is providing training workshops inontology design, development, and usage, and is also pursuing research inontology evaluation, quality, and use of ontologies to promote scientificdiscovery. Through the research activities within the Center,collaborations with the DBPs, and interactions with the biomedicalcommunity, our goal is to help scientists to work more effectively in thee-science paradigm, enhancing experiment design, experiment execution,data analysis, information synthesis, hypothesis generation and testing,and understand human disease.

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

    KAUST Repository

    Hoehndorf, Robert

    2015-01-28

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

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

    Directory of Open Access Journals (Sweden)

    Viti Federica

    2008-04-01

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

  7. An ontology for sensor networks

    Science.gov (United States)

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

    2010-05-01

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

  8. 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.

  9. 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.

  10. 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.

  11. Geo-Ontologies Are Scale Dependent

    Science.gov (United States)

    Frank, A. U.

    2009-04-01

    Philosophers aim at a single ontology that describes "how the world is"; for information systems we aim only at ontologies that describe a conceptualization of reality (Guarino 1995; Gruber 2005). A conceptualization of the world implies a spatial and temporal scale: what are the phenomena, the objects and the speed of their change? Few articles (Reitsma et al. 2003) seem to address that an ontology is scale specific (but many articles indicate that ontologies are scale-free in another sense namely that they are scale free in the link densities between concepts). The scale in the conceptualization can be linked to the observation process. The extent of the support of the physical observation instrument and the sampling theorem indicate what level of detail we find in a dataset. These rules apply for remote sensing or sensor networks alike. An ontology of observations must include scale or level of detail, and concepts derived from observations should carry this relation forward. A simple example: in high resolution remote sensing image agricultural plots and roads between them are shown, at lower resolution, only the plots and not the roads are visible. This gives two ontologies, one with plots and roads, the other with plots only. Note that a neighborhood relation in the two different ontologies also yield different results. References Gruber, T. (2005). "TagOntology - a way to agree on the semantics of tagging data." Retrieved October 29, 2005., from http://tomgruber.org/writing/tagontology-tagcapm-talk.pdf. Guarino, N. (1995). "Formal Ontology, Conceptual Analysis and Knowledge Representation." International Journal of Human and Computer Studies. Special Issue on Formal Ontology, Conceptual Analysis and Knowledge Representation, edited by N. Guarino and R. Poli 43(5/6). Reitsma, F. and T. Bittner (2003). Process, Hierarchy, and Scale. Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information ScienceInternational Conference

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

    Science.gov (United States)

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

    2015-09-01

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

  13. The role of ontologies in biological and biomedical research: a functional perspective

    KAUST Repository

    Hoehndorf, Robert

    2015-04-10

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  14. The role of ontologies in biological and biomedical research: a functional perspective.

    Science.gov (United States)

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

    2015-11-01

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  15. The MMI Device Ontology: Enabling Sensor Integration

    Science.gov (United States)

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

    2010-12-01

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

  16. Video Content Analysis Framework Based on Concept Ontology%基于概念本体的视频内容分析框架

    Institute of Scientific and Technical Information of China (English)

    张良; 周长胜

    2011-01-01

    In order to solve the video structure problem of semantic analysis,created a video content analysis framework based on concept ontology. The video is divided by the concept ontology,it summarized the concept of four typical video;category concept,object concepts, property concepts and emotional concepts. It also discusses the relationship between various concepts :instance-of,anribute-of, kind -of ,part-of. The video structured by concept ontology consistent with human cognitive processes and cognitive rules of things. The concept ontology as the center can establish good contact between the underlying feature vector and high-level semantic, to the easy mapping ,organization and processing.%为解决视频内容分析过程中对视频组织结构划分的问题,建立了一个基于概念本体的视频分析模型,将视频以概念本体的方式进行划分,归纳出视频中四种典型的概念:类别概念、对象概念、属性概念以及情感概念.论述了各类概念之间的关系:实例关系、属性关系、归类关系、组成关系.采用人工定义规则与学习方法相结合的方法,实现对视频概念本体的识别和划分.以概念本体为中心划分视频结构,符合人类认知事物过程和认知规律,便于将底层特征向量与高层语义进行映射、组织和处理.

  17. Conservativity Principle Violations for Ontology Alignment: Survey and Trends

    Directory of Open Access Journals (Sweden)

    Yahia Atig

    2016-07-01

    Full Text Available Ontology matching techniques are a solution to overcome the problem of interoperability between ontologies. However, the generated mappings suffer from logical defects that influence their usefulness. In this paper we present a detailed analysis of the problem socalled conservativity principle; alignment between ontologies should never generate new knowledge compared to those generated by reasoning solely on ontologies. We also study the sub-problems; Ontology change and Satisfiability preservation problems and compare the related works and their way to detect and repair conservativity principle. At the end we present a set of open research issues

  18. Fast Gene Ontology based clustering for microarray experiments

    OpenAIRE

    Ovaska Kristian; Laakso Marko; Hautaniemi Sampsa

    2008-01-01

    Abstract Background Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. Results We present fa...

  19. SEMANTIC INTEGRATION FOR AUTOMATIC ONTOLOGY MAPPING

    Directory of Open Access Journals (Sweden)

    Siham AMROUCH

    2013-11-01

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

  20. A Parsing Graph-based Algorithm for Ontology Mapping

    Institute of Scientific and Technical Information of China (English)

    WANG Zong-jiang; WANG Ying-lin; ZHANG Shen-sheng; DU Tao

    2009-01-01

    Ontology mapping is a critical problem for integrating the heterogeneous information sources. It can identify the elements corresponding to each other. At present, there are many ontology mapping algorithms, but most of them are bused on database schema. After analyzing the similarity and difference of ontology and schema, wepropose a parsing graph-based algorithm for ontology mapping. The ontology parsing graph (OP-graph) extends the general concept of graph, encodes logic relationship, and semantic information which the ontology contains into vertices and edges of the graph. Thus, the problem of ontology mapping is translated into a problem of finding the optimal match between the two OP-graphs. With the definition of a universal measure for comparing the entities of two ontoingies, we calculate the whole similarity between the two OP-graphs iteratively, until the optimal match is found. The results of experiments show that our algorithm is promising.

  1. Child cancer follow-up ontology and information system

    DEFF Research Database (Denmark)

    El-Subaihi, J.A.; Anton, François; Mioc, Darka

    2013-01-01

    brings the methodology for child cancer treatment plan that produces an ontology to create a conceptual model and a database model. To construct the ontology, the "methontology" method is used as a structured approach for the ontology process. The method guides the ontology developer from scratch...... to building a complete model. The ontology is developed in two phases. In the first phase, research from other countries and process models are reviewed and the generic model is built from this research. The generic model is adapted to the ontology for the Danish hospitals including the NOPHO-ALL 2008...... protocol. To develop the ontology, a data dictionary is first proposed. Then, the relationships between concepts are identified and verified: the oriented graph, where nodes are concepts and oriented edges are dependence relationships, where the definition of the concept at the origin of the edge depends...

  2. Identifiable Data Files - Medicare Provider Analysis and ...

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicare Provider Analysis and Review (MEDPAR) File contains data from claims for services provided to beneficiaries admitted to Medicare certified inpatient...

  3. Identifying Proper Names Based on Association Analysis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The issue of proper names recognition in Chinese text was discussed. An automatic approach based on association analysis to extract rules from corpus was presented. The method tries to discover rules relevant to external evidence by association analysis, without additional manual effort. These rules can be used to recognize the proper nouns in Chinese texts. The experimental result shows that our method is practical in some applications.Moreover, the method is language independent.

  4. Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

    OpenAIRE

    Zhen Li; Bi-Qing Li; Min Jiang; Lei Chen; Jian Zhang; Lin Liu; Tao Huang

    2013-01-01

    One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance...

  5. An Ontology of the Submarine Relief for Analysis and Representation on Nautical Charts

    OpenAIRE

    YAN, Jingya; Guilbert, Eric; Saux, Eric

    2013-01-01

    A nautical chart is a kind of map used to describe the seafloor morphology and shoreline of adjacent lands. One of its main purposes is to guaranty safety of navigation. As a consequence, construction of a nautical chart follows very specific rules. The cartographer has to select and highlight undersea features according to their relevance to navigation. In an automated process, the system must be able to identify and classify these features from the terrain model. This paper aims therefore a...

  6. A Survey on how Description Logic Ontologies Benefit from Formal Concept Analysis

    CERN Document Server

    Sertkaya, Baris

    2011-01-01

    Although the notion of a concept as a collection of objects sharing certain properties, and the notion of a conceptual hierarchy are fundamental to both Formal Concept Analysis and Description Logics, the ways concepts are described and obtained differ significantly between these two research areas. Despite these differences, there have been several attempts to bridge the gap between these two formalisms, and attempts to apply methods from one field in the other. The present work aims to give an overview on the research done in combining Description Logics and Formal Concept Analysis.

  7. Cosmological Ontology and Epistemology

    CERN Document Server

    Page, Don N

    2014-01-01

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

  8. Database for exchangeable gene trap clones: pathway and gene ontology analysis of exchangeable gene trap clone mouse lines.

    Science.gov (United States)

    Araki, Masatake; Nakahara, Mai; Muta, Mayumi; Itou, Miharu; Yanai, Chika; Yamazoe, Fumika; Miyake, Mikiko; Morita, Ayaka; Araki, Miyuki; Okamoto, Yoshiyuki; Nakagata, Naomi; Yoshinobu, Kumiko; Yamamura, Ken-ichi; Araki, Kimi

    2014-02-01

    Gene trapping in embryonic stem (ES) cells is a proven method for large-scale random insertional mutagenesis in the mouse genome. We have established an exchangeable gene trap system, in which a reporter gene can be exchanged for any other DNA of interest through Cre/mutant lox-mediated recombination. We isolated trap clones, analyzed trapped genes, and constructed the database for Exchangeable Gene Trap Clones (EGTC) [http://egtc.jp]. The number of registered ES cell lines was 1162 on 31 August 2013. We also established 454 mouse lines from trap ES clones and deposited them in the mouse embryo bank at the Center for Animal Resources and Development, Kumamoto University, Japan. The EGTC database is the most extensive academic resource for gene-trap mouse lines. Because we used a promoter-trap strategy, all trapped genes were expressed in ES cells. To understand the general characteristics of the trapped genes in the EGTC library, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis and found that the EGTC ES clones covered a broad range of pathways. We also used Gene Ontology (GO) classification data provided by Mouse Genome Informatics (MGI) to compare the functional distribution of genes in each GO term between trapped genes in the EGTC mouse lines and total genes annotated in MGI. We found the functional distributions for the trapped genes in the EGTC mouse lines and for the RefSeq genes for the whole mouse genome were similar, indicating that the EGTC mouse lines had trapped a wide range of mouse genes. © 2014 The Authors Development, Growth & Differentiation © 2014 Japanese Society of Developmental Biologists.

  9. Identifying Peer Institutions Using Cluster Analysis

    Science.gov (United States)

    Boronico, Jess; Choksi, Shail S.

    2012-01-01

    The New York Institute of Technology's (NYIT) School of Management (SOM) wishes to develop a list of peer institutions for the purpose of benchmarking and monitoring/improving performance against other business schools. The procedure utilizes relevant criteria for the purpose of establishing this peer group by way of a cluster analysis. The…

  10. Building a Human Health Risk Assessment Ontology (RsO): A Proposed Framework.

    Science.gov (United States)

    McKone, Thomas E; Feng, Lydia

    2015-11-01

    Over the last decade the health and environmental research communities have made significant progress in collecting and improving access to genomic, toxicology, exposure, health, and disease data useful to health risk assessment. One of the barriers to applying these growing volumes of information in fields such as risk assessment is the lack of informatics tools to organize, curate, and evaluate thousands of journal publications and hundreds of databases to provide new insights on relationships among exposure, hazard, and disease burden. Many fields are developing ontologies as a way of organizing and analyzing large amounts of complex information from multiple scientific disciplines. Ontologies include a vocabulary of terms and concepts with defined logical relationships to each other. Building from the recently published exposure ontology and other relevant health and environmental ontologies, this article proposes an ontology for health risk assessment (RsO) that provides a structural framework for organizing risk assessment information and methods. The RsO is anchored by eight major concepts that were either identified by exploratory curations of the risk literature or the exposure-ontology working group as key for describing the risk assessment domain. These concepts are: (1) stressor, (2) receptor, (3) outcome, (4) exposure event, (5) dose-response approach, (6) dose-response metric, (7) uncertainty, and (8) measure of risk. We illustrate the utility of these concepts for the RsO with example curations of published risk assessments for ionizing radiation, arsenic in drinking water, and persistent pollutants in salmon. © 2015 Society for Risk Analysis.

  11. An Ontological and Epistemological Analysis of the Presentation of the First Law of Thermodynamics in School and University Textbooks

    Science.gov (United States)

    Poblete, Joaquin Castillo; Rojas, Rocio Ogaz; Merino, Cristian; Quiroz, Waldo

    2016-01-01

    Considering the relevance of thermodynamics to the scientific discipline of chemistry and the curriculum of the Western school system, the philosophical system of Mario Bunge, particularly his ontology and epistemology, is used herein to analyze the presentation of the first law of thermodynamics in 15 school and university textbooks. The…

  12. Identifying MMORPG Bots: A Traffic Analysis Approach

    Science.gov (United States)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  13. Identifying MMORPG Bots: A Traffic Analysis Approach

    Directory of Open Access Journals (Sweden)

    Wen-Chin Chen

    2008-11-01

    Full Text Available Massively multiplayer online role playing games (MMORPGs have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1 the regularity in the release time of client commands, 2 the trend and magnitude of traffic burstiness in multiple time scales, and 3 the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  14. Identifying nonlinear biomechanical models by multicriteria analysis

    Science.gov (United States)

    Srdjevic, Zorica; Cveticanin, Livija

    2012-02-01

    In this study, the methodology developed by Srdjevic and Cveticanin (International Journal of Industrial Ergonomics 34 (2004) 307-318) for the nonbiased (objective) parameter identification of the linear biomechanical model exposed to vertical vibrations is extended to the identification of n-degree of freedom (DOF) nonlinear biomechanical models. The dynamic performance of the n-DOF nonlinear model is described in terms of response functions in the frequency domain, such as the driving-point mechanical impedance and seat-to-head transmissibility function. For randomly generated parameters of the model, nonlinear equations of motion are solved using the Runge-Kutta method. The appropriate data transformation from the time-to-frequency domain is performed by a discrete Fourier transformation. Squared deviations of the response functions from the target values are used as the model performance evaluation criteria, thus shifting the problem into the multicriteria framework. The objective weights of criteria are obtained by applying the Shannon entropy concept. The suggested methodology is programmed in Pascal and tested on a 4-DOF nonlinear lumped parameter biomechanical model. The identification process over the 2000 generated sets of parameters lasts less than 20 s. The model response obtained with the imbedded identified parameters correlates well with the target values, therefore, justifying the use of the underlying concept and the mathematical instruments and numerical tools applied. It should be noted that the identified nonlinear model has an improved accuracy of the biomechanical response compared to the accuracy of a linear model.

  15. Research on the complex network of the UNSPSC ontology

    Science.gov (United States)

    Xu, Yingying; Zou, Shengrong; Gu, Aihua; Wei, Li; Zhou, Ta

    The UNSPSC ontology mainly applies to the classification system of the e-business and governments buying the worldwide products and services, and supports the logic structure of classification of the products and services. In this paper, the related technologies of the complex network were applied to analyzing the structure of the ontology. The concept of the ontology was corresponding to the node of the complex network, and the relationship of the ontology concept was corresponding to the edge of the complex network. With existing methods of analysis and performance indicators in the complex network, analyzing the degree distribution and community of the ontology, and the research will help evaluate the concept of the ontology, classify the concept of the ontology and improve the efficiency of semantic matching.

  16. Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks.

    Science.gov (United States)

    Trinh, Hung-Cuong; Kwon, Yung-Keun

    2015-11-01

    Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.

  17. The Ontology of Disaster.

    Science.gov (United States)

    Thompson, Neil

    1995-01-01

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

  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. 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…

  20. The Ontology of Disaster.

    Science.gov (United States)

    Thompson, Neil

    1995-01-01

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

  1. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

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

  2. COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

    Science.gov (United States)

    Cui, Licong

    Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance

  3. Ayurveda research: Ontological challenges.

    Science.gov (United States)

    Nayak, Jayakrishna

    2012-01-01

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

  4. Ayurveda research: Ontological challenges

    Directory of Open Access Journals (Sweden)

    Jayakrishna Nayak

    2012-01-01

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

  5. An improved method for functional similarity analysis of genes based on Gene Ontology.

    Science.gov (United States)

    Tian, Zhen; Wang, Chunyu; Guo, Maozu; Liu, Xiaoyan; Teng, Zhixia

    2016-12-23

    Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional similarity methods have been proposed based on the semantic similarity of GO terms. However, these leading approaches may make errorprone judgments especially when they measure the specificity of GO terms as well as the IC of a term set. Therefore, how to estimate the gene functional similarity reliably is still a challenging problem. We propose WIS, an effective method to measure the gene functional similarity. First of all, WIS computes the IC of a term by employing its depth, the number of its ancestors as well as the topology of its descendants in the GO graph. Secondly, WIS calculates the IC of a term set by means of considering the weighted inherited semantics of terms. Finally, WIS estimates the gene functional similarity based on the IC overlap ratio of term sets. WIS is superior to some other representative measures on the experiments of functional classification of genes in a biological pathway, collaborative evaluation of GO-based semantic similarity measures, protein-protein interaction prediction and correlation with gene expression. Further analysis suggests that WIS takes fully into account the specificity of terms and the weighted inherited semantics of terms between GO terms. The proposed WIS method is an effective and reliable way to compare gene function. The web service of WIS is freely available at http://nclab.hit.edu.cn/WIS/ .

  6. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    Science.gov (United States)

    2011-01-01

    Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA. Conclusions GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches. PMID:21914205

  7. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    Directory of Open Access Journals (Sweden)

    Kirsten Toralf

    2011-09-01

    Full Text Available Abstract Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA. Conclusions GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.

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

    Directory of Open Access Journals (Sweden)

    Smith Barry

    2010-06-01

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

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

    NARCIS (Netherlands)

    J.W. Stoelhorst

    2008-01-01

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

  10. An ontology for major histocompatibility restriction.

    Science.gov (United States)

    Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

    2016-01-01

    MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

  11. Ontological Matchmaking in Recommender Systems

    CERN Document Server

    Bonifati, Angela; Sileo, Domenica; Summa, Gianvito

    2010-01-01

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

  12. [ ] Toward an Ontology of Finitude

    Directory of Open Access Journals (Sweden)

    Julia Hölzl

    2011-09-01

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

  13. Using Ontology Fingerprints to Evaluate Genome-wide Association Results

    OpenAIRE

    Lam Tsoi; Michael Boehnke; Richard Klein; Jim Zheng

    2009-01-01

    We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach...

  14. 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

  15. The sexual and ontology

    Directory of Open Access Journals (Sweden)

    Zupančič Alenka

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-02-04

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

  17. Towards automated biomedical ontology harmonization.

    Science.gov (United States)

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

    2014-01-01

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

  18. Building Integrated Ontological Knowledge Structures with Efficient Approximation Algorithms

    Directory of Open Access Journals (Sweden)

    Yang Xiang

    2015-01-01

    Full Text Available The integration of ontologies builds knowledge structures which brings new understanding on existing terminologies and their associations. With the steady increase in the number of ontologies, automatic integration of ontologies is preferable over manual solutions in many applications. However, available works on ontology integration are largely heuristic without guarantees on the quality of the integration results. In this work, we focus on the integration of ontologies with hierarchical structures. We identified optimal structures in this problem and proposed optimal and efficient approximation algorithms for integrating a pair of ontologies. Furthermore, we extend the basic problem to address the integration of a large number of ontologies, and correspondingly we proposed an efficient approximation algorithm for integrating multiple ontologies. The empirical study on both real ontologies and synthetic data demonstrates the effectiveness of our proposed approaches. In addition, the results of integration between gene ontology and National Drug File Reference Terminology suggest that our method provides a novel way to perform association studies between biomedical terms.

  19. 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.

  20. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    2013-01-01

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

  1. Ontological Enrichment of the Genes-to-Systems Breast Cancer Database

    Science.gov (United States)

    Viti, Federica; Mosca, Ettore; Merelli, Ivan; Calabria, Andrea; Alfieri, Roberta; Milanesi, Luciano

    Breast cancer research need the development of specific and suitable tools to appropriately manage biomolecular knowledge. The presented work deals with the integrative storage of breast cancer related biological data, in order to promote a system biology approach to this network disease. To increase data standardization and resource integration, annotations maintained in Genes-to-Systems Breast Cancer (G2SBC) database are associated to ontological terms, which provide a hierarchical structure to organize data enabling more effective queries, statistical analysis and semantic web searching. Exploited ontologies, which cover all levels of the molecular environment, from genes to systems, are among the most known and widely used bioinformatics resources. In G2SBC database ontology terms both provide a semantic layer to improve data storage, accessibility and analysis and represent a user friendly instrument to identify relations among biological components.

  2. The Development of Ontology from Multiple Databases

    Science.gov (United States)

    Kasim, Shahreen; Aswa Omar, Nurul; Fudzee, Mohd Farhan Md; Azhar Ramli, Azizul; Aizi Salamat, Mohamad; Mahdin, Hairulnizam

    2017-08-01

    The area of halal industry is the fastest growing global business across the world. The halal food industry is thus crucial for Muslims all over the world as it serves to ensure them that the food items they consume daily are syariah compliant. Currently, ontology has been widely used in computer sciences area such as web on the heterogeneous information processing, semantic web, and information retrieval. However, ontology has still not been used widely in the halal industry. Today, Muslim community still have problem to verify halal status for products in the market especially foods consisting of E number. This research tried to solve problem in validating the halal status from various halal sources. There are various chemical ontology from multilple databases found to help this ontology development. The E numbers in this chemical ontology are codes for chemicals that can be used as food additives. With this E numbers ontology, Muslim community could identify and verify the halal status effectively for halal products in the market.

  3. 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…

  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. Network analysis identifies common genes associated with obesity in six obesity-related diseases*

    OpenAIRE

    Su, Li-ning; Wang, Yan-bing; Wnag, Chun-guang; Wei, Hui-ping

    2017-01-01

    Obesity has been reported to be associated with many diseases. However, common obesity-induced biological processes have not been evaluated across these diseases. We identified genes associated with obesity and obesity-related diseases, and used them to construct protein‒protein interaction networks. We also analyzed gene ontology (GO) in those genes overlapping between obesity and disease. Our work identifies gene modules common to obesity and obesity-related diseases, which can provide a ba...

  6. Ontologies for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Agnieszka Leszczynski

    2008-01-01

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

  7. Mechanisms in biomedical ontology

    National Research Council Canada - National Science Library

    Röhl, Johannes

    2012-01-01

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

  8. Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

    Science.gov (United States)

    Ochs, Christopher; Perl, Yehoshua; Geller, James; Haendel, Melissa; Brush, Matthew; Arabandi, Sivaram; Tu, Samson

    2015-08-01

    Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such unwanted side effects often go unnoticed since biomedical ontologies are large and complex knowledge structures. Abstraction networks, which provide compact summaries of an ontology's content and structure, have been used to uncover structural irregularities, inconsistencies and errors in ontologies. In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology release. A Diff AbN can be used to support curators in identifying unintended and unwanted ontology changes. The derivation of two Diff AbNs, the Diff Area Taxonomy and the Diff Partial-area Taxonomy, is explained and Diff Partial-area Taxonomies are derived and analyzed for the Ontology of Clinical Research, Sleep Domain Ontology, and eagle-i Research Resource Ontology. Diff Taxonomy usage for identifying unintended erroneous consequences of quality assurance and ontology merging are demonstrated. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. The relevance of ontological commitments

    CERN Document Server

    Echenique-Robba, Pablo

    2014-01-01

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

  10. Manufacturing ontology through templates

    Directory of Open Access Journals (Sweden)

    Diciuc Vlad

    2017-01-01

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

  11. An Ontology of Gene

    OpenAIRE

    Masuya, Hiroshi; Mizoguchi, Riichiro

    2012-01-01

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

  12. Ontology alignment with OLA

    OpenAIRE

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

    2004-01-01

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

  13. Ontology Usage at ZFIN

    CERN Document Server

    Howe, Doug

    2010-01-01

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

  14. Applications of ontology design patterns in biomedical ontologies.

    Science.gov (United States)

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

    2012-01-01

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

  15. Applications of Ontology Design Patterns in Biomedical Ontologies

    Science.gov (United States)

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

    2012-01-01

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

  16. Analysis and reasoning of knowledge based on ontology of colleges and universities%基于本体的高校知识分析和推理

    Institute of Scientific and Technical Information of China (English)

    袁小艳

    2014-01-01

    以高校知识为研究和应用背景,研究基于本体理论的高校知识本体结构化表示和描述,并采用protege 4.0建立了高校知识本体。同时从高校知识中提取出基本公理、类内公理和类间公理,建立公理库,并采用protege的PAL推理引擎对高校知识进行一致性分析和推理。解决了高校知识语义层次上的信息共享和交互的问题,为高校知识的管理提供语义支撑。%With knowledge of colleges and universities as the research and application background,the university knowl-edge ontology structuring representation and description based on the theory of the ontology are studied. Protege4.0 is adopted to establish the university knowledge ontology. The axiom library was established by extracting the basic axioms,class axiom and axioms between classes from university knowledge. The PAL inference engine of Protege is used to do consistency analysis and reasoning of university knowledge. The information sharing and interaction in the semantic level of knowledge in colleges and uni-versities was realized. It provided a semantic support for knowledge management of colleges and universities.

  17. The Ontology of the Gene Ontology

    Science.gov (United States)

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

    2003-01-01

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

  18. GFVO: the Genomic Feature and Variation Ontology.

    Science.gov (United States)

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

    2015-01-01

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

  19. The neologism ontoi in Broussais's condemnation of medical ontology.

    Science.gov (United States)

    Bole, T J

    1995-10-01

    This note uses an analysis of Broussais's objection to medical ontology to suggest why Broussais's neologism ontoi is derived not from onta but from a conflation of onta and the plural of ogkos. For Broussais medical ontology, in contrast to philosophical ontology, always refers to abstract entities alleged to explain sensible symptoms, ogkoi, in the sense of indivisible particles in the writings of Lucretius and Epicurus, are such particles; onta are not.

  20. Microposts Ontology Construction Via Concept Extraction

    Directory of Open Access Journals (Sweden)

    Beenu Yadav

    2012-08-01

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

  1. Ontology modeling for generation of clinical pathways

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    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

  2. Biomedical imaging ontologies: A survey and proposal for future work

    Directory of Open Access Journals (Sweden)

    Barry Smith

    2015-01-01

    Full Text Available Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as "cell" or "image" or "tissue" or "microscope" that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.

  3. Gene expression patterns combined with network analysis identify hub genes associated with bladder cancer.

    Science.gov (United States)

    Bi, Dongbin; Ning, Hao; Liu, Shuai; Que, Xinxiang; Ding, Kejia

    2015-06-01

    To explore molecular mechanisms of bladder cancer (BC), network strategy was used to find biomarkers for early detection and diagnosis. The differentially expressed genes (DEGs) between bladder carcinoma patients and normal subjects were screened using empirical Bayes method of the linear models for microarray data package. Co-expression networks were constructed by differentially co-expressed genes and links. Regulatory impact factors (RIF) metric was used to identify critical transcription factors (TFs). The protein-protein interaction (PPI) networks were constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and clusters were obtained through molecular complex detection (MCODE) algorithm. Centralities analyses for complex networks were performed based on degree, stress and betweenness. Enrichment analyses were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Co-expression networks and TFs (based on expression data of global DEGs and DEGs in different stages and grades) were identified. Hub genes of complex networks, such as UBE2C, ACTA2, FABP4, CKS2, FN1 and TOP2A, were also obtained according to analysis of degree. In gene enrichment analyses of global DEGs, cell adhesion, proteinaceous extracellular matrix and extracellular matrix structural constituent were top three GO terms. ECM-receptor interaction, focal adhesion, and cell cycle were significant pathways. Our results provide some potential underlying biomarkers of BC. However, further validation is required and deep studies are needed to elucidate the pathogenesis of BC. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Science.gov (United States)

    Wang, Ying; Ding, Jia-Tong; Yang, Hai-Ming; Yan, Zheng-Jie; Cao, Wei; Li, Yang-Bai

    2015-01-01

    Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp) were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  5. Analysis of Pigeon (Columba Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  6. ``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.

  7. Overview of Ontology Servers Research

    Directory of Open Access Journals (Sweden)

    Robert M. Colomb

    2007-06-01

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

  8. Empirical Phenomenon, Subjective Construction And Ontological Trught: (An Analysis of Problems of Scientific Explanation and Critical Realism Approach

    Directory of Open Access Journals (Sweden)

    Faramarz Taghilou

    2014-12-01

    Full Text Available Both the positivist and negativist frameworks of explanation are common in this naturalist proposition that unlike the metaphysical philosophy, reality is embedded only in experimental level. Therefore, the scientific explanation of natural and social phenomenon should refer to this experimental level in order to be called meaningful, verifiable and scientific. But, the problem was always that the principle of causality as a necessary condition for every kind of scientific explanation is not logically deductible from induction in experimental level and remains as a metaphysical principle. The principle of experimental objectivity as a condition for the verifiability clause of scientific explanations could not be defended, because the experimentation was always embedded in subjectivity and theory. The Kantian idealists, in contrast, considering the scientific explanation as a mere representation of reality in subjective categories, could not justify the experimental knowledge of reality and the rationality for comparison among theories and paradigms. Critical Realism as an important approach in philosophy of science that relates to the works and thoughts of Roy Bhaskar tries to solve these problems by resorting to its principles of ontological realism, epistemological relativism, and judgmental rationality. Considering and analyzing the scientific explanation’s issues, we have focused here on the answers of the Critical Realism in this case. We will argue that how the Critical Realist interpretation of scientific explanation, the experimental phenomenon, and the subjective construction and ontological reality all reach to a logical coherence with each other.

  9. Multi-tissue microarray analysis identifies a molecular signature of regeneration.

    Directory of Open Access Journals (Sweden)

    Sarah E Mercer

    Full Text Available The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine.

  10. Multi-Tissue Microarray Analysis Identifies a Molecular Signature of Regeneration

    Science.gov (United States)

    Mercer, Sarah E.; Cheng, Chia-Ho; Atkinson, Donald L.; Krcmery, Jennifer; Guzman, Claudia E.; Kent, David T.; Zukor, Katherine; Marx, Kenneth A.; Odelberg, Shannon J.; Simon, Hans-Georg

    2012-01-01

    The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine. PMID:23300656

  11. Query strategy for sequential ontology debugging

    CERN Document Server

    Shchekotykhina, Kostyantyn; Fleiss, Philipp; Rodler, Patrick

    2011-01-01

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

  12. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

    Directory of Open Access Journals (Sweden)

    Jesús Lascorz

    2011-01-01

    Full Text Available Background: A large number of gene expression profiling (GEP studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-regulated in colorectal carcinogenesis. Materials and Methods: We started the analysis with 242 unique annotated genes that had been reported by any of three recent meta-analyses covering GEP studies on genes differentially expressed in carcinoma vs normal mucosa. Most of these genes (218, 91.9% had been reported in at least three GEP studies. These 242 genes were submitted to bioinformatic analysis using a total of nine tools to detect enrichment of Gene Ontology (GO categories or Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. As a final consistency criterion the pathway categories had to be enriched by several tools to be taken into consideration. Results: Our pathway-based enrichment analysis identified the categories of ribosomal protein constituents, extracellular matrix receptor interaction, carbonic anhydrase isozymes, and a general category related to inflammation and cellular response as significantly and consistently overrepresented entities. Conclusions: We triaged the genes covered by the published GEP literature on colorectal carcinogenesis and subjected them to multiple enrichment tools in order to identify the consistently enriched gene categories. These turned out to have known functional relationships to cancer development and thus deserve further investigation.

  13. An Object-Oriented Metamodel for Bunge-Wand-Weber Ontology

    CERN Document Server

    Kiwelekar, Arvind W

    2010-01-01

    A UML based metamodel for Bunge-Wand-Weber (BWW) ontology is presented. BWW ontology is a generic framework for analysis and conceptualization of real world objects. It includes categories that can be applied to analyze and classify objects found in an information system. In the context of BWW ontology, the metamodel is a representation of the ontological categories and relationships among them. An objective behind developing an object-oriented metamodel has been to model BWW ontology in terms of widely used notions in software development. The main contributions of this paper are a classification for ontological categories, a description template, and representations through UML and typed based models.

  14. 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.

  15. Formal Ontology: Foundation of Domain Knowledge Sharing and Reusing

    Institute of Scientific and Technical Information of China (English)

    陆汝钤; 金芝

    2002-01-01

    Domain analysis is the activity of identifying and representing the relevantinformation in a domain, so that the information can be shared and reused in similar systems.But until now, no efficient approaches are available for capturing and representing the results ofdomain analysis and then for sharing and reusing the domain knowledge. This paper proposesan ontology-oriented approach for formalizing the domain models. The architecture for themultiple-layer structure of the domain knowledge base is also discussed. And finally, somegenetic algorithm-based methods have been given for supporting the knowledge sharing andreusing.

  16. On the ontology based representation of cell lines.

    Directory of Open Access Journals (Sweden)

    Matthias Ganzinger

    Full Text Available Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.

  17. 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.

  18. Using MathML to Represent Units of Measurement for Improved Ontology Alignment

    NARCIS (Netherlands)

    Do, C.; Pauwels, E.J.

    2013-01-01

    Ontologies provide a formal description of concepts and their relationships in a knowledge domain. The goal of ontology alignment is to identify semantically matching concepts and relationships across independently developed ontologies that purport to describe the same knowledge. In order to handle

  19. Ontology Based Access Control

    Directory of Open Access Journals (Sweden)

    Özgü CAN

    2010-02-01

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

  20. A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: the case of OBO disease ontologies.

    Science.gov (United States)

    Marquet, Gwenaëlle; Mosser, Jean; Burgun, Anita

    2007-12-01

    The OBO ontologies include more than 50 standard vocabularies that cover different domains, including genomics, chemistry, anatomy and phenotype. Ontology alignment is a means to build consistent biomedical ontologies compatible with standard vocabularies and dedicated to specific domains, such as cancer. An alignment is defined as a set of pairs of concepts, coming from two ontologies, related by a relation R, R not being restricted to the equivalence or subsumption relations. Alignment is performed in three major steps: first, the concepts that are equivalent in the ontologies are identified; second the pairs of concepts that are related although not equivalent are searched for; third the relations between the concepts are characterized. We have developed a method to align ontologies that exploits the compositionality of the terms in OBO ontologies, uses the UMLS to provide synonyms and relations, and defines syntactico-semantic patterns that characterize semantically the relations between concepts. We have applied it to four OBO phenotype ontologies: mouse pathology, human disease, mammalian phenotype, and PATO. We found 386 pairs of equivalent concepts and 20,461 pairs of concepts where one concept name is included in the other term. Among the 20,460 inclusions, we were able to provide a semantic categorization for 2682 relations. In 2552 cases, the relation was present and semantically defined in the UMLS Metathesaurus, in 131 cases the relation was characterized through semantic patterns. Our approach may help to find the semantic relations between concepts in ontologies.

  1. OTO: Ontology Term Organizer.

    Science.gov (United States)

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

    2015-02-15

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

  2. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

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

  3. GFVO: the Genomic Feature and Variation Ontology

    Directory of Open Access Journals (Sweden)

    Joachim Baran

    2015-05-01

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

  4. Appreciating ontological struggles

    DEFF Research Database (Denmark)

    Danholt, Peter

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

  5. 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

  6. Annotating Evidence Based Clinical Guidelines: A Lightweight Ontology

    NARCIS (Netherlands)

    R. Hoekstra; A. de Waard; R. Vdovjak

    2012-01-01

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

  7. 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....

  8. Ontology development for Sufism domain

    Science.gov (United States)

    Iqbal, Rizwan

    2012-01-01

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

  9. An Architectural Approach for Building Medical Ontologies

    Directory of Open Access Journals (Sweden)

    Mircea Adrian FOCŞA

    2016-07-01

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

  10. OWL应用接口的比较分析%Comparative Analysis of APIs for OWL Ontology

    Institute of Scientific and Technical Information of China (English)

    熊振辉; 于娟

    2015-01-01

    The paper comparatively analyzes three types of APIs for OWL, including Jena API、Protégé API and OWL API, from aspects of characteristics, platforms which they base on, languages which they can process and OWL ontology models. It focuses on commonly-used functions of OWL API and obtains related conclusions: (1) Jena API cannot achieve all functions of OWL because it bases on RDF triple;(2) OWL API is specifically designed for OWL and it supports structural specification of OWL2 which is the latest edition of OWL;(3) current APIs for OWL ontology mostly base on Java platform, whereas APIs base on other platforms (e.g. .net plat-form) have not appeared.%比较分析了Jena API、Protégé API、OWL API这三种OWL应用接口(API)的特点、所基于的平台、可处理的语言以及描述OWL本体的模型,重点介绍了OWL API的常用基本功能,得出了相关结论:(1)Jena API基于RDF三元组的特点使其不能实现OWL语言的全部功能;(2)OWL API针对OWL语言设计,且支持最新的OWL2语言的结构规范;(3)目前这些API都是基于Java平台的,对于其它平台(如.net平台),尚未见有成熟的API出现。

  11. Co-expression Analysis Identifies CRC and AP1 the Regulator of Arabidopsis Fatty Acid Biosynthesis

    Institute of Scientific and Technical Information of China (English)

    Xinxin Han; Linlin Yin; Hongwei Xue

    2012-01-01

    Fatty acids (FAs) play crucial rules in signal transduction and plant development,however,the regulation of FA metabolism is still poorly understood.To study the relevant regulatory network,fifty-eight FA biosynthesis genes including de novo synthases,desaturases and elongases were selected as "guide genes" to construct the co-expression network.Calculation of the correlation between all Arabidopsis thaliana (L.) genes with each guide gene by Arabidopsis co-expression dating mining tools (ACT)identifies 797 candidate FA-correlated genes.Gene ontology (GO) analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism,and function in many processes.Interestingly,63 transcription factors (TFs) were identified as candidate FA biosynthesis regulators and 8 TF families are enriched.Two TF genes,CRC and AP1,both correlating with 8 FA guide genes,were further characterized.Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds.The contents of palmitoleic acid,stearic acid,arachidic acid and eicosadienoic acid are decreased,whereas that of oleic acid is increased in ap1 and crc seeds,which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes.In addition,yeast one-hybrid analysis and electrophoretic mobility shift assay (EMSA) revealed that CRC can bind to the promoter regions of KCS7 and KCS15,indicating that CRC may directly regulate FA biosynthesis.

  12. Identifying clinical course patterns in SMS data using cluster analysis

    DEFF Research Database (Denmark)

    Kent, Peter; Kongsted, Alice

    2012-01-01

    ABSTRACT: BACKGROUND: Recently, there has been interest in using the short message service (SMS or text messaging), to gather frequent information on the clinical course of individual patients. One possible role for identifying clinical course patterns is to assist in exploring clinically importa...... of cluster analysis. More research is needed, especially head-to-head studies, to identify which technique is best to use under what circumstances.......ABSTRACT: BACKGROUND: Recently, there has been interest in using the short message service (SMS or text messaging), to gather frequent information on the clinical course of individual patients. One possible role for identifying clinical course patterns is to assist in exploring clinically important...... by spline analysis. However, cluster analysis of SMS data in its original untransformed form may be simpler and offer other advantages. Therefore, the aim of this study was to determine whether cluster analysis could be used for identifying clinical course patterns distinct from the pattern of the whole...

  13. Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells

    Science.gov (United States)

    Rines, Daniel R; Gomez-Ferreria, Maria Ana; Zhou, Yingyao; DeJesus, Paul; Grob, Seanna; Batalov, Serge; Labow, Marc; Huesken, Dieter; Mickanin, Craig; Hall, Jonathan; Reinhardt, Mischa; Natt, Francois; Lange, Joerg; Sharp, David J; Chanda, Sumit K; Caldwell, Jeremy S

    2008-01-01

    Background The mitotic spindle is a complex mechanical apparatus required for accurate segregation of sister chromosomes during mitosis. We designed a genetic screen using automated microscopy to discover factors essential for mitotic progression. Using a RNA interference library of 49,164 double-stranded RNAs targeting 23,835 human genes, we performed a loss of function screen to look for small interfering RNAs that arrest cells in metaphase. Results Here we report the identification of genes that, when suppressed, result in structural defects in the mitotic spindle leading to bent, twisted, monopolar, or multipolar spindles, and cause cell cycle arrest. We further describe a novel analysis methodology for large-scale RNA interference datasets that relies on supervised clustering of these genes based on Gene Ontology, protein families, tissue expression, and protein-protein interactions. Conclusion This approach was utilized to classify functionally the identified genes in discrete mitotic processes. We confirmed the identity for a subset of these genes and examined more closely their mechanical role in spindle architecture. PMID:18302737

  14. Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion

    Directory of Open Access Journals (Sweden)

    Huang XiaoDong

    2008-06-01

    Full Text Available Abstract Background High throughput screens with RNA interference technology enable loss-of-function analyses of gene activities in mammalian cells. While the construction of genome-scale shRNA libraries has been successful, results of large-scale screening of those libraries can be difficult to analyze because of the relatively high noise levels and the fact that not all shRNAs in a library are equally effective in silencing gene expression. Results We have screened a library consisting of 43,828 shRNAs directed against 8,500 human genes for functions that are necessary in cell detachment induced by a constitutively activated c-Abl tyrosine kinase. To deal with the issues of noise and uncertainty of knockdown efficiencies, we employed an analytical strategy that combines quantitative data analysis with biological knowledge, i.e. Gene Ontology and pathway information, to increase the power of the RNAi screening technique. Using this strategy we found 16 candidate genes to be involved in Abl-induced disruption of cell adhesion, and verified that the knockdown of IL6ST is associated with enhanced cell attachment. Conclusion Our results suggest that the power of genome-wide quantitative shRNA screens can be significantly increased when analyzed using a systems biology-based approach to identify functional gene networks.

  15. De Novo Transcriptome Analysis of Allium cepa L. (Onion Bulb to Identify Allergens and Epitopes.

    Directory of Open Access Journals (Sweden)

    Hemalatha Rajkumar

    Full Text Available Allium cepa (onion is a diploid plant with one of the largest nuclear genomes among all diploids. Onion is an example of an under-researched crop which has a complex heterozygous genome. There are no allergenic proteins and genomic data available for onions. This study was conducted to establish a transcriptome catalogue of onion bulb that will enable us to study onion related genes involved in medicinal use and allergies. Transcriptome dataset generated from onion bulb using the Illumina HiSeq 2000 technology showed a total of 99,074,309 high quality raw reads (~20 Gb. Based on sequence homology onion genes were categorized into 49 different functional groups. Most of the genes however, were classified under 'unknown' in all three gene ontology categories. Of the categorized genes, 61.2% showed metabolic functions followed by cellular components such as binding, cellular processes; catalytic activity and cell part. With BLASTx top hit analysis, a total of 2,511 homologous allergenic sequences were found, which had 37-100% similarity with 46 different types of allergens existing in the database. From the 46 contigs or allergens, 521 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. This is the first comprehensive insight into the transcriptome of onion bulb tissue using the NGS technology, which can be used to map IgE epitopes and prediction of structures and functions of various proteins.

  16. De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes.

    Science.gov (United States)

    Rajkumar, Hemalatha; Ramagoni, Ramesh Kumar; Anchoju, Vijayendra Chary; Vankudavath, Raju Naik; Syed, Arshi Uz Zaman

    2015-01-01

    Allium cepa (onion) is a diploid plant with one of the largest nuclear genomes among all diploids. Onion is an example of an under-researched crop which has a complex heterozygous genome. There are no allergenic proteins and genomic data available for onions. This study was conducted to establish a transcriptome catalogue of onion bulb that will enable us to study onion related genes involved in medicinal use and allergies. Transcriptome dataset generated from onion bulb using the Illumina HiSeq 2000 technology showed a total of 99,074,309 high quality raw reads (~20 Gb). Based on sequence homology onion genes were categorized into 49 different functional groups. Most of the genes however, were classified under 'unknown' in all three gene ontology categories. Of the categorized genes, 61.2% showed metabolic functions followed by cellular components such as binding, cellular processes; catalytic activity and cell part. With BLASTx top hit analysis, a total of 2,511 homologous allergenic sequences were found, which had 37-100% similarity with 46 different types of allergens existing in the database. From the 46 contigs or allergens, 521 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. This is the first comprehensive insight into the transcriptome of onion bulb tissue using the NGS technology, which can be used to map IgE epitopes and prediction of structures and functions of various proteins.

  17. An ontological view of advanced practice nursing.

    Science.gov (United States)

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

    2005-01-01

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

  18. 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. Visualizing the temporal distribution of terminologies for biological ontology development

    Science.gov (United States)

    Kim, Tak-eun; Lee, Hodong; Park, Jinah; Park, Jong C.

    2008-01-01

    Communities in biology have developed a number of ontologies that provide standard terminologies for the characteristics of various concepts and their relationships. However, it is difficult to construct and maintain such ontologies in biology, since it is a non-trivial task to identify commonly used potential member terms in a particular ontology, in the presence of constant changes of such terms over time as the research in the field advances. In this paper, we propose a visualization system, called BioTermViz, which presents the temporal distribution of ontological terms from the text of published journal abstracts. BioTermViz shows such a temporal distribution of terms for journal abstracts in the order of published time, occurrences of the annotated Gene Ontology concepts per abstract, and the ontological hierarchy of the terms. With a combination of these three types of information, we can capture the global tendency in the use of terms, and identify a particular term or terms to be created, modified, segmented, or removed, effectively developing biological ontologies in an interactive manner. In order to demonstrate the practical utility of BioTermViz, we describe several scenarios for the development of an ontology for a specific sub-class of proteins, or ubiquitin-protein ligases.

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

    Science.gov (United States)

    Ong, Edison; He, Yongqun

    2016-01-01

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

  1. 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…

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

    OpenAIRE

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

    2008-01-01

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

  4. Automatic Learning of Ontologies for the Semantic Web: experiment lexical learning

    OpenAIRE

    2012-01-01

    This paper proposes the design of a System for Automatic Learning of Ontologies and Lexical Information (SALOX) for the Dynamic Semantic Ontological Framework for the Semantic Web (DSOFSW). DSOFSW interprets query in natural language (Spanish) to the web, and is composed by five parts; a linguistic ontology for the grammar of Spanish, a lexicon for the lexical information, a database of facts about the system experiences, a task ontology for the linguistic analysis process, and an interpretat...

  5. 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

  6. Feature-opinion pair identification of product reviews in Chinese: a domain ontology modeling method

    Science.gov (United States)

    Yin, Pei; Wang, Hongwei; Guo, Kaiqiang

    2013-03-01

    With the emergence of the new economy based on social media, a great amount of consumer feedback on particular products are conveyed through wide-spreading product online reviews, making opinion mining a growing interest for both academia and industry. According to the characteristic mode of expression in Chinese, this research proposes an ontology-based linguistic model to identify the basic appraisal expression in Chinese product reviews-"feature-opinion pair (FOP)." The product-oriented domain ontology is constructed automatically at first, then algorithms to identify FOP are designed by mapping product features and opinions to the conceptual space of the domain ontology, and finally comparative experiments are conducted to evaluate the model. Experimental results indicate that the performance of the proposed approach in this paper is efficient in obtaining a more accurate result compared to the state-of-art algorithms. Furthermore, through identifying and analyzing FOPs, the unstructured product reviews are converted into structured and machine-sensible expression, which provides valuable information for business application. This paper contributes to the related research in opinion mining by developing a solid foundation for further sentiment analysis at a fine-grained level and proposing a general way for automatic ontology construction.

  7. Ontology-based application integration

    CERN Document Server

    Paulheim, Heiko

    2011-01-01

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

  8. Integrated Analysis Identifies Molecular Signatures and Specific Prognostic Factors for Different Gastric Cancer Subtypes

    Directory of Open Access Journals (Sweden)

    Li Min

    2017-02-01

    Full Text Available BACKGROUND: Gastric cancer (GC is the fifth leading cause of cancer-related deaths worldwide. As an effective and easily performed method, microscopy-based Lauren classification has been widely accepted by gastrointestinal surgeons and pathologists for GC subtyping, but molecular characteristics of different Lauren subtypes were poorly revealed. METHODS: GSE62254 was used as a derivation cohort, and GSE15459 was used as a validation cohort. The difference between diffuse and intestinal GC on the gene expression level was measured. Gene ontology (GO enrichment analysis was performed for both subgroups. Hierarchical clustering and heatmap exhibition were also performed. Kaplan-Meier plot and Cox proportional hazards model were used to evaluate survival grouped by the given genes or hierarchical clusters. RESULTS: A total of 4598 genes were found differentially expressed between diffuse and intestinal GC. Immunity- and cell adhesion–related GOs were enriched for diffuse GC, whereas DNA repair– and cell cycle–related GOs were enriched for intestinal GC. We proposed a 40-gene signature (χ2 = 30.71, P < .001 that exhibits better discrimination for prognosis than Lauren classification (χ2 = 12.11, P = .002. FRZB [RR (95% CI = 1.824 (1.115-2.986, P = .017] and EFEMP1 [RR (95% CI = 1.537 (0.969-2.437, P = .067] were identified as independent prognostic factors only in diffuse GC but not in intestinal GC patients. KRT23 [RR (95% CI = 1.616 (0.938-2.785, P = .083] was identified as an independent prognostic factor only in intestinal GC patients but not in diffuse GC patients. Similar results were achieved in the validation cohort. CONCLUSION: We found that GCs with different Lauren classifications had different molecular characteristics and identified FRZB, EFEMP1, and KRT23 as subtype-specific prognostic factors for GC patients.

  9. What Four Million Mappings Can Tell You about Two Hundred Ontologies

    Science.gov (United States)

    Ghazvinian, Amir; Noy, Natalya F.; Jonquet, Clement; Shah, Nigam; Musen, Mark A.

    The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal—an open community-based repository of biomedical ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of concept names and synonyms. We then analyzed the mappings and what they tell us about the ontologies themselves, the structure of the ontology repository, and the ways in which the mappings can help in the process of ontology design and evaluation. For example, we can use the mappings to guide users who are new to a field to the most pertinent ontologies in that field, to identify areas of the domain that are not covered sufficiently by the ontologies in the repository, and to identify which ontologies will serve well as background knowledge in domain-specific tools. While we used a specific (but large) ontology repository for the study, we believe that the lessons we learned about the value of a large-scale set of mappings to ontology users and developers are general and apply in many other domains.

  10. Toward a formal ontology for narrative

    Directory of Open Access Journals (Sweden)

    Ciotti, Fabio

    2016-03-01

    Full Text Available In this paper the rationale and the first draft of a formal ontology for modeling narrative texts are presented. Building on the semiotic and structuralist narratology, and on the work carried out in the late 1980s by Giuseppe Gigliozzi in Italy, the focus of my research are the concepts of character and of narrative world/space. This formal model is expressed in the OWL 2 ontology language. The main reason to adopt a formal modeling approach is that I consider the purely probabilistic-quantitative methods (now widespread in digital literary studies inadequate. An ontology, on one hand provides a tool for the analysis of strictly literary texts. On the other hand (though beyond the scope of the present work, its formalization can also represent a significant contribution towards grounding the application of storytelling methods outside of scholarly contexts.

  11. Ontology-enriched Visualization of Human Anatomy

    Energy Technology Data Exchange (ETDEWEB)

    Pouchard, LC

    2005-12-20

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

  12. Modelling the cybersecurity environment using morphological ontology design engineering

    CSIR Research Space (South Africa)

    Jansen van Vuuren, JC

    2015-03-01

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

  13. Exploring biomedical ontology mappings with graph theory methods

    National Research Council Canada - National Science Library

    Simon Kocbek; Jin-Dong Kim

    2017-01-01

    .... Methods We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points...

  14. 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.

  15. Benchmarking Ontologies: Bigger or Better?

    Science.gov (United States)

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

    2011-01-01

    A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them. PMID:21249231

  16. Benchmarking ontologies: bigger or better?

    Science.gov (United States)

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

    2011-01-13

    A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.

  17. OWL 2 learn profile: an ontology sublanguage for the learning domain.

    Science.gov (United States)

    Heiyanthuduwage, Sudath R; Schwitter, Rolf; Orgun, Mehmet A

    2016-01-01

    Many experimental ontologies have been developed for the learning domain for use at different institutions. These ontologies include different OWL/OWL 2 (Web Ontology Language) constructors. However, it is not clear which OWL 2 constructors are the most appropriate ones for designing ontologies for the learning domain. It is possible that the constructors used in these learning domain ontologies match one of the three standard OWL 2 profiles (sublanguages). To investigate whether this is the case, we have analysed a corpus of 14 ontologies designed for the learning domain. We have also compared the constructors used in these ontologies with those of the OWL 2 RL profile, one of the OWL 2 standard profiles. The results of our analysis suggest that the OWL 2 constructors used in these ontologies do not exactly match the standard OWL 2 RL profile, but form a subset of that profile which we call OWL 2 Learn.

  18. K-GATE Ontology Driven Knowledge Based System for Decision Support

    Directory of Open Access Journals (Sweden)

    Pavel Gardavsky

    2012-01-01

    Full Text Available The purpose of this paper is to describe a practical solution how to build an ontology driven knowledge based system for decision support about a domain of interest. Topic Maps standardized techniques were used for ontology building and also for keeping ontology open for new requirements. After detailed evaluation process, AToM2 software product was chosen for ontology development. Besides ontology development AToM2 provides complex tools for normalizing data into ontology both in interactive/automated way, mining knowledge from the ontology and presenting results. Software product Tovek Server was used for analysing and determining useful and domain relevant structures in unstructured content. The resulting knowledge based system is created as an output of methodological processes called Coordinated Analysis and Sharing of Information. The resulting Ontology Driven Knowledge Based System for Decision Support proposal was named K-GATE.

  19. Automatic background knowledge selection for matching biomedical ontologies.

    Directory of Open Access Journals (Sweden)

    Daniel Faria

    Full Text Available Ontology matching is a growing field of research that is of critical importance for the semantic web initiative. The use of background knowledge for ontology matching is often a key factor for success, particularly in complex and lexically rich domains such as the life sciences. However, in most ontology matching systems, the background knowledge sources are either predefined by the system or have to be provided by the user. In this paper, we present a novel methodology for automatically selecting background knowledge sources for any given ontologies to match. This methodology measures the usefulness of each background knowledge source by assessing the fraction of classes mapped through it over those mapped directly, which we call the mapping gain. We implemented this methodology in the AgreementMakerLight ontology matching framework, and evaluate it using the benchmark biomedical ontology matching tasks from the Ontology Alignment Evaluation Initiative (OAEI 2013. In each matching problem, our methodology consistently identified the sources of background knowledge that led to the highest improvements over the baseline alignment (i.e., without background knowledge. Furthermore, our proposed mapping gain parameter is strongly correlated with the F-measure of the produced alignments, thus making it a good estimator for ontology matching techniques based on background knowledge.

  20. Making methodology a matter of process ontology

    DEFF Research Database (Denmark)

    Revsbæk, Line

    2016-01-01

    This paper presents a practice of doing qualitative interview analysis from the insights of the process ontology in G. H. Mead’s Philosophy of the Present (1932). The paper presents two cases of analyzing in the present while listening to recorded interview material eliciting researcher’s case st...

  1. Activity theories and the ontology of psychology

    DEFF Research Database (Denmark)

    Mammen, Jens Skaun; Mironenko, Irina

    2015-01-01

    to exceed some, mostly implicit, ontological restrictions in traditional AT and free it from an embracement of functionalism and mechanicism, rooted in Renaissance Physics. The analysis goes back to Aristotle’s understanding of the freely moving animal in its ecology and introduces some dualities...

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

  4. Structural parameter identifiability analysis for dynamic reaction networks

    DEFF Research Database (Denmark)

    Davidescu, Florin Paul; Jørgensen, Sten Bay

    2008-01-01

    . The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...... method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...

  5. Biomedical ontologies: a functional perspective.

    Science.gov (United States)

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

    2008-01-01

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

  6. Infrastructures as Ontological Experiments

    Directory of Open Access Journals (Sweden)

    Casper Bruun Jensen

    2015-11-01

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

  7. ONTOLOGY: UNREAL REALITY

    Directory of Open Access Journals (Sweden)

    Piotr Jaroszynski

    2014-12-01

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

  8. FROG - Fingerprinting Genomic Variation Ontology.

    Directory of Open Access Journals (Sweden)

    E Abinaya

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

  9. BIOELECTRICAL IMPEDANCE VECTOR ANALYSIS IDENTIFIES SARCOPENIA IN NURSING HOME RESIDENTS

    Science.gov (United States)

    Loss of muscle mass and water shifts between body compartments are contributing factors to frailty in the elderly. The body composition changes are especially pronounced in institutionalized elderly. We investigated the ability of single-frequency bioelectrical impedance analysis (BIA) to identify b...

  10. Identifying subgroups of patients using latent class analysis

    DEFF Research Database (Denmark)

    Nielsen, Anne Mølgaard; Kent, Peter; Hestbæk, Lise

    2017-01-01

    BACKGROUND: Heterogeneity in patients with low back pain (LBP) is well recognised and different approaches to subgrouping have been proposed. Latent Class Analysis (LCA) is a statistical technique that is increasingly being used to identify subgroups based on patient characteristics. However, as ...

  11. 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…

  12. 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

  13. Ontology Partitioning: Clustering Based Approach

    Directory of Open Access Journals (Sweden)

    Soraya Setti Ahmed

    2015-05-01

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

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

    Lifescience Database Archive (English)

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

  15. Identification of canine platelet proteins separated by differential detergent fractionation for nonelectrophoretic proteomics analyzed by Gene Ontology and pathways analysis

    Directory of Open Access Journals (Sweden)

    Trichler SA

    2014-01-01

    Full Text Available Shauna A Trichler,1,* Sandra C Bulla,1,* Nandita Mahajan,1 Kari V Lunsford,2 Ken Pendarvis,3 Bindu Nanduri,4,5 Fiona M McCarthy,3 Camilo Bulla1 1Department of Pathobiology and Population Medicine, 2Department of Clinical Sciences and Animal Health Center, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 3Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ, 4Department of Biological Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 5Institute for Genomics, Biocomputing and Biotechnology, Starkville, MS, USA *These authors contributed equally to this work Abstract: During platelet development, proteins necessary for the many functional roles of the platelet are stored within cytoplasmic granules. Platelets have also been shown to take up and store many plasma proteins into granules. This makes the platelet a potential novel source of biomarkers for many disease states. Approaches to sample preparation for proteomic studies for biomarkers search vary. Compared with traditional two-dimensional polyacrylamide gel electrophoresis systems, nonelectrophoretic proteomics methods that employ offline protein fractionation methods such as the differential detergent fractionation method have clear advantages. Here we report a proteomic survey of the canine platelet proteome using differential detergent fractionation coupled with mass spectrometry and functional modeling of the canine platelet proteins identified. A total of 5,974 unique proteins were identified from platelets, of which only 298 (5% had previous experimental evidence of in vivo expression. The use of offline prefractionation of canine proteins by differential detergent fractionation resulted in greater proteome coverage as compared with previous reports. This initial study contributes to a broader understanding of canine platelet biology and aids functional research

  16. Identifying glioblastoma gene networks based on hypergeometric test analysis.

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    Vasileios Stathias

    Full Text Available Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA. To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in tumors resected from patients suffering from the most common malignant adult brain tumor, glioblastoma (GBM. We performed RNA sequencing on tumors from individual GBM patients and filtered the results through the TCGA database in order to identify possible gene networks that are overrepresented in GBM samples relative to controls. Importantly, we demonstrate that hypergeometric-based analysis of gene pairs identifies gene networks that validate experimentally. These studies identify a putative workflow for uncovering differentially expressed patient specific genes and gene networks for GBM and other cancers.

  17. Rehabilitation robotics ontology on the cloud.

    Science.gov (United States)

    Dogmus, Zeynep; Papantoniou, Agis; Kilinc, Muhammed; Yildirim, Sibel A; Erdem, Esra; Patoglu, Volkan

    2013-06-01

    We introduce the first formal rehabilitation robotics ontology, called RehabRobo-Onto, to represent information about rehabilitation robots and their properties; and a software system RehabRobo-Query to facilitate access to this ontology. RehabRobo-Query is made available on the cloud, utilizing Amazon Web services, so that 1) rehabilitation robot designers around the world can add/modify information about their robots in RehabRobo-Onto, and 2) rehabilitation robot designers and physical medicine experts around the world can access the knowledge in RehabRobo-Onto by means of questions about robots, in natural language, with the guide of the intelligent userinterface of RehabRobo-Query. The ontology system consisting of RehabRobo-Onto and RehabRobo-Query is of great value to robot designers as well as physical therapists and medical doctors. On the one hand, robot designers can access various properties of the existing robots and to the related publications to further improve the state-of-the-art. On the other hand, physical therapists and medical doctors can utilize the ontology to compare rehabilitation robots and to identify the ones that serve best to cover their needs, or to evaluate the effects of various devices for targeted joint exercises on patients with specific disorders.

  18. Biomedical ontologies: a functional perspective

    National Research Council Canada - National Science Library

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

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

  19. 生物医学本体工程进展%Current Status of Biomedical Ontology Engineering

    Institute of Scientific and Technical Information of China (English)

    于彤; 崔蒙; 杨硕; 李敬华; 刘丽红; 贾李蓉

    2012-01-01

    近年来,领域本体在生物医学领域广泛应用,在知识的获取、管理和检索中发挥了积极作用.通过文献调研找出了生物医学领域中的本体,选取其中的代表性本体进行调研与分析,并讨论了存在的问题和发展趋势.%In recent years, a variety of domain ontologies have been developed in biomedical domain. They are playing an important role in the acquisition, management, and retrieval of biomedical knowledge. We identify biomedica] ontologies through literature review, and select a set of representative ontologies for investigation and analysis. We also discuss the open problems and trends in this field.

  20. Detecting Inconsistencies in the Gene Ontology Using Ontology Databases with Not-gadgets

    Science.gov (United States)

    Lependu, Paea; Dou, Dejing; Howe, Doug

    We present ontology databases with not-gadgets, a method for detecting inconsistencies in an ontology with large numbers of annotated instances by using triggers and exclusion dependencies in a unique way. What makes this work relevant is the use of the database itself, rather than an external reasoner, to detect logical inconsistencies given large numbers of annotated instances. What distinguishes this work is the use of event-driven triggers together with the introduction of explicit negations. We applied this approach toward the serotonin example, an open problem in biomedical informatics which aims to use annotations to help identify inconsistencies in the Gene Ontology. We discovered 75 inconsistencies that have important implications in biology, which include: (1) methods for refining transfer rules used for inferring electronic annotations, and (2) highlighting possible biological differences across species worth investigating.

  1. Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism.

    Directory of Open Access Journals (Sweden)

    Jian Zheng

    Full Text Available Syringa oblata Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of S. oblata are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp, 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in S. oblata, providing a useful database for further research on S. oblata and other plants of genus Syringa.

  2. An Approach for Ontology Integration for Personalization with the Support of XML

    Directory of Open Access Journals (Sweden)

    S.Vigneshwari

    2014-01-01

    Full Text Available Ontological way of knowledge representation is very much useful to the semantic web. In the modernized computer era, there is a need of a special technique for personalization. XML plays an important role in information retrieval systems and XML being a common format for information interpretation, it will be easy to understand as well as easy to construct. In this paper, a framework has been proposed for personalizing the web using XML based ontologies. This framework needs integration between global ontology and locally generated ontology based on user profiles. The relevant concepts between both the ontologies are identified, grouped together and ranked. Finally, the generated ontologies are evaluated using standard datasets, based on their semantic structures. The clustered concepts and query pairs are being analyzed with varying threshold limits. In addition, the performance metrics show that the ontology based techniques show a good precision, recall values for the user given data, when compared to text-based approaches.

  3. Latent cluster analysis of ALS phenotypes identifies prognostically differing groups.

    Directory of Open Access Journals (Sweden)

    Jeban Ganesalingam

    Full Text Available BACKGROUND: Amyotrophic lateral sclerosis (ALS is a degenerative disease predominantly affecting motor neurons and manifesting as several different phenotypes. Whether these phenotypes correspond to different underlying disease processes is unknown. We used latent cluster analysis to identify groupings of clinical variables in an objective and unbiased way to improve phenotyping for clinical and research purposes. METHODS: Latent class cluster analysis was applied to a large database consisting of 1467 records of people with ALS, using discrete variables which can be readily determined at the first clinic appointment. The model was tested for clinical relevance by survival analysis of the phenotypic groupings using the Kaplan-Meier method. RESULTS: The best model generated five distinct phenotypic classes that strongly predicted survival (p<0.0001. Eight variables were used for the latent class analysis, but a good estimate of the classification could be obtained using just two variables: site of first symptoms (bulbar or limb and time from symptom onset to diagnosis (p<0.00001. CONCLUSION: The five phenotypic classes identified using latent cluster analysis can predict prognosis. They could be used to stratify patients recruited into clinical trials and generating more homogeneous disease groups for genetic, proteomic and risk factor research.

  4. Identifying influential factors of business process performance using dependency analysis

    Science.gov (United States)

    Wetzstein, Branimir; Leitner, Philipp; Rosenberg, Florian; Dustdar, Schahram; Leymann, Frank

    2011-02-01

    We present a comprehensive framework for identifying influential factors of business process performance. In particular, our approach combines monitoring of process events and Quality of Service (QoS) measurements with dependency analysis to effectively identify influential factors. The framework uses data mining techniques to construct tree structures to represent dependencies of a key performance indicator (KPI) on process and QoS metrics. These dependency trees allow business analysts to determine how process KPIs depend on lower-level process metrics and QoS characteristics of the IT infrastructure. The structure of the dependencies enables a drill-down analysis of single factors of influence to gain a deeper knowledge why certain KPI targets are not met.

  5. Constructing a Geology Ontology Using a Relational Database

    Science.gov (United States)

    Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

    2013-12-01

    In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances

  6. An Ontology Based Approach to Implement the Online Recommendation System

    Directory of Open Access Journals (Sweden)

    Vijayakumar Mohanraj

    2011-01-01

    Full Text Available Problem statement: Every web user has different intent when accessing the information on website. The primary goal of recommendation system is to anticipate the user intent and recommend the web pages that contain user expected information. Effective recommendation of web pages involves two important challenges: accurately identifying the user intent and predict the result show that novel web usage mining method and ontological concept scoring algorithm based on website domain ontological profile helps the recommendation system imminent navigation pattern in such a way that it provides required content while users browse the predicted navigation. Approach: We present a ontology based approach to implement recommendation system that involves applying innovative web usage mining on log system to discover all possible imminent navigation patterns of current user and resolve any uncertainties in discovering the navigation pattern by applying ontological concept based similarity comparison and scoring algorithm. Results: result show that novel web usage mining method and ontological concept scoring algorithm based on website domain ontological profile helps the recommendation system to predict and present most relevant navigation pattern to users. Conclusion: our recommendation system confirms that ontology based approach should be used to ensure excellent accuracy in predicting and capturing future navigation pattern of web user.

  7. 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

  8. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

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

  9. The organization ontology

    OpenAIRE

    2014-01-01

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

  10. 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.

  11. Identifying Organizational Inefficiencies with Pictorial Process Analysis (PPA

    Directory of Open Access Journals (Sweden)

    David John Patrishkoff

    2013-11-01

    Full Text Available Pictorial Process Analysis (PPA was created by the author in 2004. PPA is a unique methodology which offers ten layers of additional analysis when compared to standard process mapping techniques.  The goal of PPA is to identify and eliminate waste, inefficiencies and risk in manufacturing or transactional business processes at 5 levels in an organization. The highest level being assessed is the process management, followed by the process work environment, detailed work habits, process performance metrics and general attitudes towards the process. This detailed process assessment and analysis is carried out during process improvement brainstorming efforts and Kaizen events. PPA creates a detailed visual efficiency rating for each step of the process under review.  A selection of 54 pictorial Inefficiency Icons (cards are available for use to highlight major inefficiencies and risks that are present in the business process under review. These inefficiency icons were identified during the author's independent research on the topic of why things go wrong in business. This paper will highlight how PPA was developed and show the steps required to conduct Pictorial Process Analysis on a sample manufacturing process. The author has successfully used PPA to dramatically improve business processes in over 55 different industries since 2004.  

  12. Educational Advertising Ontology: A Domain-Dependent Ontology for Semantic Advertising Networks

    Directory of Open Access Journals (Sweden)

    Lilac A.E. Al-Safadi

    2010-01-01

    Full Text Available Problem statement: Currently advertising networks connects Web site owners (Publishers that want to host advertisements with advertisers who want to run advertisements. Advertising networks' reliance on only the keywords in the content without an accurate interpretation of the context of the page, results in displaying irrelevant and unappealing ads on the web page. Approach: Ontologies provided a shared and common understanding of a domain that can be communicated between people and across application systems. Our objective was to create a domain-dependent Ontology to play a major role in supporting information exchange processes in semantic advertising networks. Results: Results for the prototype of matching ads with publishers had been presented in terms of precision and recall. High precision was shown and analysis of results was given in detail. Conclusion: The proposed Ontology is effective for advertising networks at a semantic level.

  13. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

    Science.gov (United States)

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-03-09

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in L-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport--NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885--were also expressed at significantly higher levels in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, L-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.

  14. Ontology through a Mindfulness Process

    Science.gov (United States)

    Bearance, Deborah; Holmes, Kimberley

    2015-01-01

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

  15. Ontological turns, turnoffs and roundabouts.

    Science.gov (United States)

    Sismondo, Sergio

    2015-06-01

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

  16. A Temporal Web Ontology Language

    NARCIS (Netherlands)

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

    2009-01-01

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

  17. 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.…

  18. Ontology Based Model Transformation Infrastructure

    NARCIS (Netherlands)

    Göknil, A.; Topaloglu, N.Y.

    2005-01-01

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

  19. Building Ontologies in DAML + OIL

    Science.gov (United States)

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

    2003-01-01

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

  20. 一种基于模糊形式概念分析的模糊本体学习方法%A FUZZY ONTOLOGY LEARNING METHOD BASED ON FUZZY FORMAL CONCEPT ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    马迪; 李冠宇

    2014-01-01

    模糊本体是语义网中处理模糊信息的重要工具,而模糊本体学习是构建模糊本体的一种有效方法,因此模糊本体学习已逐渐成为现今本体研究的热点。作为模糊本体的另一种图结构的表现形式,模糊概念格构造与演化的研究也渐渐引起人们的关注。模糊形式概念分析是一种基于模糊形式背景表示形式概念的新模型,是由模糊集理论与形式概念分析结合而成,其主要表现形式即是模糊概念格。这种模糊概念层次结构是数据分析及规则提取的有效工具,且支持概念间相似度的计算。提出一种基于模糊形式概念分析的模糊本体学习方法,意图从领域文档中获取模糊概念和模糊概念关系,并通过模糊形式概念分析,将其添加到源模糊本体转化的模糊概念格中,以完成模糊本体学习。%Fuzzy ontology is an important tool used to deal with fuzzy information in semantic Web,while fuzzy ontology learning is an ef-fective method to construct the fuzzy ontology,therefore it has gradually become the focus in current ontology research.As another graph-structured manifestation of fuzzy ontology,the studies on the construction and evolution of fuzzy concept lattice are also increasingly attractedscholarsattentions.Fuzzy formal concept analysis is a new model which employs fuzzy formal background to represent formal concepts,and isthe integration of fuzzy set theory and the formal concept analysis,its major manifestation is the fuzzy concept lattice.This fuzzy concept hier-archical structure is an effective tool for data analysis and rule extraction and supports the inter-concept similarity calculation.With the inten-tion to acquire fuzzy concepts and fuzzy concept relations from domain documents,in the paper we propose a fuzzy ontology learning methodwhich is based on fuzzy formal concept analysis,and add it to fuzzy concept lattice transformed from source fuzzy

  1. Ontology-based Information Retrieval

    DEFF Research Database (Denmark)

    Styltsvig, Henrik Bulskov

    of concept similarity in query evaluation is discussed. A semantic expansion approach that incorporates concept similarity is introduced and a generalized fuzzy set retrieval model that applies expansion during query evaluation is presented. While not commonly used in present information retrieval systems......In this thesis, we will present methods for introducing ontologies in information retrieval. The main hypothesis is that the inclusion of conceptual knowledge such as ontologies in the information retrieval process can contribute to the solution of major problems currently found in information...... retrieval. This utilization of ontologies has a number of challenges. Our focus is on the use of similarity measures derived from the knowledge about relations between concepts in ontologies, the recognition of semantic information in texts and the mapping of this knowledge into the ontologies in use...

  2. Data Migration for Ontology Evolution

    Institute of Scientific and Technical Information of China (English)

    赵彦; 张雷; 林晨曦; 张卓; 俞勇

    2004-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  4. Identifying Sources of Difference in Reliability in Content Analysis

    Directory of Open Access Journals (Sweden)

    Elizabeth Murphy

    2005-07-01

    Full Text Available This paper reports on a case study which identifies and illustrates sources of difference in agreement in relation to reliability in a context of quantitative content analysis of a transcript of an online asynchronous discussion (OAD. Transcripts of 10 students in a month-long online asynchronous discussion were coded by two coders using an instrument with two categories, five processes, and 19 indicators of Problem Formulation and Resolution (PFR. Sources of difference were identified in relation to: coders; tasks; and students. Reliability values were calculated at the levels of categories, processes, and indicators. At the most detailed level of coding on the basis of the indicator, findings revealed that the overall level of reliability between coders was .591 when measured with Cohen’s kappa. The difference between tasks at the same level ranged from .349 to .664, and the difference between participants ranged from .390 to .907. Implications for training and research are discussed.

  5. Proteogenomic Analysis Identifies a Novel Human SHANK3 Isoform

    Directory of Open Access Journals (Sweden)

    Fahad Benthani

    2015-05-01

    Full Text Available Mutations of the SHANK3 gene have been associated with autism spectrum disorder. Individuals harboring different SHANK3 mutations display considerable heterogeneity in their cognitive impairment, likely due to the high SHANK3 transcriptional diversity. In this study, we report a novel interaction between the Mutated in colorectal cancer (MCC protein and a newly identified SHANK3 protein isoform in human colon cancer cells and mouse brain tissue. Hence, our proteogenomic analysis identifies a new human long isoform of the key synaptic protein SHANK3 that was not predicted by the human reference genome. Taken together, our findings describe a potential new role for MCC in neurons, a new human SHANK3 long isoform and, importantly, highlight the use of proteomic data towards the re-annotation of GC-rich genomic regions.

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

    Directory of Open Access Journals (Sweden)

    Lili Zhang

    2014-02-01

    Full Text Available Digital learning resource ontology is often based on different specification building. It is hard to find resources by linguistic ontology matching method. The existing structural matching method fails to solve the problem of calculation of structural similarity well. For the heterogeneity problem among learning resource ontology, an algorithm is presented based on subgraph approximate isomorphism. First of all, we can preprocess the resource of clustering algorithm through the semantic analysis, then describe the ontology by the directed graph and calculate the similarity, and finally judge the semantic relations through calculating and analyzing different resource between the ontology of different learning resource to achieve semantic compatibility or mapping of ontology. This method is an extension of existing methods in ontology matching. Under the comprehensive application of features such as edit distance and hierarchical relations, the similarity of graph structures between two ontologies is calculated. And, the ontology matching is determined on the condition of subgraph approximate isomorphism based on the alternately mapping of nodes and arcs in the describing graphs of ontologies. An example is used to demonstrate this ontology matching process and the time complexity is analyzed to explain its effectiveness

  7. Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis.

    Science.gov (United States)

    Wei, Jinfen; Liu, Baosuo; Fan, Sigang; Li, Haimei; Chen, Mingqiang; Zhang, Bo; Su, Jiaqi; Meng, Zihao; Yu, Dahui

    2017-03-01

    The pearl oyster Pinctada fucata is commonly cultured for marine pearls in China. To culture pearls, a mantle piece from a donor pearl oyster is grafted with a nucleus into a receptor. This transplanted mantle piece may be rejected by the immune system of the recipient oyster, thus reducing the success of transplantation. However, there have been limited studies about the oyster's immune defense against allograft. In this study, hemocyte transcriptome analysis was performed to detect the immune responses to allograft in P. fucata at 0 h and 48 h after a transplant. The sequencing reaction produced 92.5 million reads that were mapped against the reference genome sequences of P. fucata. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify all immune-related differentially expressed genes (DEGs). Compared with patterns at 0 h, a total of 798 DEGs were identified, including 410 up-regulated and 388 down-regulated genes at 48 h. The expression levels of interleukin receptor and toll-like receptor in hemocytes were increased significantly 48 h post-transplant, indicating that the oyster immune response was induced. Finally, altered levels of 18 randomly selected immune-related DEGs were confirmed by quantitative real-time PCR (qRT-PCR). Our results provide the basis for further analysis of the immune rejection of allotransplantation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Reuse of termino-ontological resources and text corpora for building a multilingual domain ontology: an application to Alzheimer's disease.

    Science.gov (United States)

    Dramé, Khadim; Diallo, Gayo; Delva, Fleur; Dartigues, Jean François; Mouillet, Evelyne; Salamon, Roger; Mougin, Fleur

    2014-04-01

    Ontologies are useful tools for sharing and exchanging knowledge. However ontology construction is complex and often time consuming. In this paper, we present a method for building a bilingual domain ontology from textual and termino-ontological resources intended for semantic annotation and information retrieval of textual documents. This method combines two approaches: ontology learning from texts and the reuse of existing terminological resources. It consists of four steps: (i) term extraction from domain specific corpora (in French and English) using textual analysis tools, (ii) clustering of terms into concepts organized according to the UMLS Metathesaurus, (iii) ontology enrichment through the alignment of French and English terms using parallel corpora and the integration of new concepts, (iv) refinement and validation of results by domain experts. These validated results are formalized into a domain ontology dedicated to Alzheimer's disease and related syndromes which is available online (http://lesim.isped.u-bordeaux2.fr/SemBiP/ressources/ontoAD.owl). The latter currently includes 5765 concepts linked by 7499 taxonomic relationships and 10,889 non-taxonomic relationships. Among these results, 439 concepts absent from the UMLS were created and 608 new synonymous French terms were added. The proposed method is sufficiently flexible to be applied to other domains.

  9. Lidar point density analysis: implications for identifying water bodies

    Science.gov (United States)

    Worstell, Bruce B.; Poppenga, Sandra; Evans, Gayla A.; Prince, Sandra

    2014-01-01

    Most airborne topographic light detection and ranging (lidar) systems operate within the near-infrared spectrum. Laser pulses from these systems frequently are absorbed by water and therefore do not generate reflected returns on water bodies in the resulting void regions within the lidar point cloud. Thus, an analysis of lidar voids has implications for identifying water bodies. Data analysis techniques to detect reduced lidar return densities were evaluated for test sites in Blackhawk County, Iowa, and Beltrami County, Minnesota, to delineate contiguous areas that have few or no lidar returns. Results from this study indicated a 5-meter radius moving window with fewer than 23 returns (28 percent of the moving window) was sufficient for delineating void regions. Techniques to provide elevation values for void regions to flatten water features and to force channel flow in the downstream direction also are presented.

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

    CERN Document Server

    Serrano Orozco, J Martín

    2012-01-01

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

  11. 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

  12. Loopy: The Political Ontology of Bipolar Disorder

    Directory of Open Access Journals (Sweden)

    RACHEL JANE LIEBERT

    2013-01-01

    Full Text Available This essay is at once a critical analysis, an experiment in form, and – with some irony – a cautionary tale. Triggered by the inclusion of prodromal diagnoses in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders, and the recent call by the United States’ (U.S. Obama administration for increased mental health screening, I argue that shifts toward identifying and intervening on one’s potential madness, or risk, circulate with/in the contemporary U.S. climate of intensified discipline and terror, and use Bipolar Disorder as a site to critically explore how and with what implications this circulation occurs. Specifically, I weave Massumi’s ‘political ontology of threat’ with the narrative of a woman diagnosed with Bipolar Disorder in order to trace the pre-emptive politics and affective logic of a risk-based approach to madness. I contend that the diagnosing and drugging of potential is a self-perpetuating loop that is personally and politically harmful, and consider alternatives to this burgeoning practice.

  13. Use of discriminant analysis to identify propensity for purchasing properties

    Directory of Open Access Journals (Sweden)

    Ricardo Floriani

    2015-03-01

    Full Text Available Properties usually represent a milestone for people and families due to the high added-value when compared with family income. The objective of this study is the proposition of a discrimination model, by a discriminant analysis of people with characteristics (according to independent variables classified as potential buyers of properties, as well as to identify the interest in the use of such property, if it will be assigned to housing or leisure activities such as a cottage or beach house, and/or for investment. Thus, the following research question is proposed: What are the characteristics that better describe the profile of people which intend to acquire properties? The study justifies itself by its economic relevance in the real estate industry, as well as to the players of the real estate Market that may develop products based on the profile of potential customers. As a statistical technique, discriminant analysis was applied to the data gathered by questionnaire, which was sent via e-mail. Three hundred and thirty four responses were gathered. Based on this study, it was observed that it is possible to identify the intention for acquired properties, as well the purpose for acquiring it, for housing or investments.

  14. Cluster analysis of clinical data identifies fibromyalgia subgroups.

    Directory of Open Access Journals (Sweden)

    Elisa Docampo

    Full Text Available INTRODUCTION: Fibromyalgia (FM is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. MATERIAL AND METHODS: 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. RESULTS: VARIABLES CLUSTERED INTO THREE INDEPENDENT DIMENSIONS: "symptomatology", "comorbidities" and "clinical scales". Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1, high symptomatology and comorbidities (Cluster 2, and high symptomatology but low comorbidities (Cluster 3, showing differences in measures of disease severity. CONCLUSIONS: We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment.

  15. Lentiviral gene ontology (LeGO) vectors equipped with novel drug-selectable fluorescent proteins: new building blocks for cell marking and multi-gene analysis.

    Science.gov (United States)

    Weber, K; Mock, U; Petrowitz, B; Bartsch, U; Fehse, B

    2010-04-01

    Vector-encoded fluorescent proteins (FPs) facilitate unambiguous identification or sorting of gene-modified cells by fluorescence-activated cell sorting (FACS). Exploiting this feature, we have recently developed lentiviral gene ontology (LeGO) vectors (www.LentiGO-Vectors.de) for multi-gene analysis in different target cells. In this study, we extend the LeGO principle by introducing 10 different drug-selectable FPs created by fusing one of the five selection marker (protecting against blasticidin, hygromycin, neomycin, puromycin and zeocin) and one of the five FP genes (Cerulean, eGFP, Venus, dTomato and mCherry). All tested fusion proteins allowed both fluorescence-mediated detection and drug-mediated selection of LeGO-transduced cells. Newly generated codon-optimized hygromycin- and neomycin-resistance genes showed improved expression as compared with their ancestors. New LeGO constructs were produced at titers >10(6) per ml (for non-concentrated supernatants). We show efficient combinatorial marking and selection of various cells, including mesenchymal stem cells, simultaneously transduced with different LeGO constructs. Inclusion of the cytomegalovirus early enhancer/chicken beta-actin promoter into LeGO vectors facilitated robust transgene expression in and selection of neural stem cells and their differentiated progeny. We suppose that the new drug-selectable markers combining advantages of FACS and drug selection are well suited for numerous applications and vector systems. Their inclusion into LeGO vectors opens new possibilities for (stem) cell tracking and functional multi-gene analysis.

  16. Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis

    Institute of Scientific and Technical Information of China (English)

    Kai; Shi; Zhi-Tong; Bing; Gui-Qun; Cao; Ling; Guo; Ya-Na; Cao; Hai-Ou; Jiang; Mei-Xia; Zhang

    2015-01-01

    AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.

  17. Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis

    Directory of Open Access Journals (Sweden)

    Kai Shi

    2015-04-01

    Full Text Available AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis (WGCNA is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study. METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus (GEO database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes. The function of the genes were annotated by gene ontology (GO. RESULTS: In this study, we identified four co-expression modules significantly correlated with clinic traits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location (sclera and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter (LTD. Additionally, we identified the hug gene (top connectivity with other genes in each module. The hub gene RPS15A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma. CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.

  18. Metabolomic analysis identifies altered metabolic pathways in Multiple Sclerosis.

    Science.gov (United States)

    Poddighe, Simone; Murgia, Federica; Lorefice, Lorena; Liggi, Sonia; Cocco, Eleonora; Marrosu, Maria Giovanna; Atzori, Luigi

    2017-07-16

    Multiple sclerosis (MS) is a chronic, demyelinating disease that affects the central nervous system and is characterized by a complex pathogenesis and difficult management. The identification of new biomarkers would be clinically useful for more accurate diagnoses and disease monitoring. Metabolomics, the identification of small endogenous molecules, offers an instantaneous molecular snapshot of the MS phenotype. Here the metabolomic profiles (utilizing plasma from patients with MS) were characterized with a Gas cromatography-mass spectrometry-based platform followed by a multivariate statistical analysis and comparison with a healthy control (HC) population. The obtained partial least square discriminant analysis (PLS-DA) model identified and validated significant metabolic differences between individuals with MS and HC (R2X=0.223, R2Y=0.82, Q2=0.562; p<0.001). Among discriminant metabolites phosphate, fructose, myo-inositol, pyroglutamate, threonate, l-leucine, l-asparagine, l-ornithine, l-glutamine, and l-glutamate were correctly identified, and some resulted as unknown. A receiver operating characteristic (ROC) curve with AUC 0.84 (p=0.01; CI: 0.75-1) generated with the concentrations of the discriminant metabolites, supported the strength of the model. Pathway analysis indicated asparagine and citrulline biosynthesis as the main canonical pathways involved in MS. Changes in the citrulline biosynthesis pathway suggests the involvement of oxidative stress during neuronal damage. The results confirmed metabolomics as a useful approach to better understand the pathogenesis of MS and to provide new biomarkers for the disease to be used together with clinical data. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  20. Genome wide transcriptome analysis of dendritic cells identifies genes with altered expression in psoriasis.

    Directory of Open Access Journals (Sweden)

    Kata Filkor

    Full Text Available Activation of dendritic cells by different pathogens induces the secretion of proinflammatory mediators resulting in local inflammation. Importantly, innate immunity must be properly controlled, as its continuous activation leads to the development of chronic inflammatory diseases such as psoriasis. Lipopolysaccharide (LPS or peptidoglycan (PGN induced tolerance, a phenomenon of transient unresponsiveness of cells to repeated or prolonged stimulation, proved valuable model for the study of chronic inflammation. Thus, the aim of this study was the identification of the transcriptional diversity of primary human immature dendritic cells (iDCs upon PGN induced tolerance. Using SAGE-Seq approach, a tag-based transcriptome sequencing method, we investigated gene expression changes of primary human iDCs upon stimulation or restimulation with Staphylococcus aureus derived PGN, a widely used TLR2 ligand. Based on the expression pattern of the altered genes, we identified non-tolerizeable and tolerizeable genes. Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (Kegg analysis showed marked enrichment of immune-, cell cycle- and apoptosis related genes. In parallel to the marked induction of proinflammatory mediators, negative feedback regulators of innate immunity, such as TNFAIP3, TNFAIP8, Tyro3 and Mer are markedly downregulated in tolerant cells. We also demonstrate, that the expression pattern of TNFAIP3 and TNFAIP8 is altered in both lesional, and non-lesional skin of psoriatic patients. Finally, we show that pretreatment of immature dendritic cells with anti-TNF-α inhibits the expression of IL-6 and CCL1 in tolerant iDCs and partially releases the suppression of TNFAIP8. Our findings suggest that after PGN stimulation/restimulation the host cell utilizes different mechanisms in order to maintain critical balance between inflammation and tolerance. Importantly, the transcriptome sequencing of stimulated/restimulated iDCs identified

  1. Cluster Analysis to Identify Possible Subgroups in Tinnitus Patients.

    Science.gov (United States)

    van den Berge, Minke J C; Free, Rolien H; Arnold, Rosemarie; de Kleine, Emile; Hofman, Rutger; van Dijk, J Marc C; van Dijk, Pim

    2017-01-01

    In tinnitus treatment, there is a tendency to shift from a "one size fits all" to a more individual, patient-tailored approach. Insight in the heterogeneity of the tinnitus spectrum might improve the management of tinnitus patients in terms of choice of treatment and identification of patients with severe mental distress. The goal of this study was to identify subgroups in a large group of tinnitus patients. Data were collected from patients with severe tinnitus complaints visiting our tertiary referral tinnitus care group at the University Medical Center Groningen. Patient-reported and physician-reported variables were collected during their visit to our clinic. Cluster analyses were used to characterize subgroups. For the selection of the right variables to enter in the cluster analysis, two approaches were used: (1) variable reduction with principle component analysis and (2) variable selection based on expert opinion. Various variables of 1,783 tinnitus patients were included in the analyses. Cluster analysis (1) included 976 patients and resulted in a four-cluster solution. The effect of external influences was the most discriminative between the groups, or clusters, of patients. The "silhouette measure" of the cluster outcome was low (0.2), indicating a "no substantial" cluster structure. Cluster analysis (2) included 761 patients and resulted in a three-cluster solution, comparable to the first analysis. Again, a "no substantial" cluster structure was found (0.2). Two cluster analyses on a large database of tinnitus patients revealed that clusters of patients are mostly formed by a different response of external influences on their disease. However, both cluster outcomes based on this dataset showed a poor stability, suggesting that our tinnitus population comprises a continuum rather than a number of clearly defined subgroups.

  2. IDOMAL: an ontology for malaria

    Directory of Open Access Journals (Sweden)

    Topalis Pantelis

    2010-08-01

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

  3. Operational Plan Ontology Model for Interconnection and Interoperability

    Science.gov (United States)

    Long, F.; Sun, Y. K.; Shi, H. Q.

    2017-03-01

    Aiming at the assistant decision-making system’s bottleneck of processing the operational plan data and information, this paper starts from the analysis of the problem of traditional expression and the technical advantage of ontology, and then it defines the elements of the operational plan ontology model and determines the basis of construction. Later, it builds up a semi-knowledge-level operational plan ontology model. Finally, it probes into the operational plan expression based on the operational plan ontology model and the usage of the application software. Thus, this paper has the theoretical significance and application value in the improvement of interconnection and interoperability of the operational plan among assistant decision-making systems.

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

    Science.gov (United States)

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

    2010-01-01

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

  5. Ontologies in medicinal chemistry: current status and future challenges.

    Science.gov (United States)

    Gómez-Pérez, Asunción; Martínez-Romero, Marcos; Rodríguez-González, Alejandro; Vázquez, Guillermo; Vázquez-Naya, José M

    2013-01-01

    Recent years have seen a dramatic increase in the amount and availability of data in the diverse areas of medicinal chemistry, making it possible to achieve significant advances in fields such as the design, synthesis and biological evaluation of compounds. However, with this data explosion, the storage, management and analysis of available data to extract relevant information has become even a more complex task that offers challenging research issues to Artificial Intelligence (AI) scientists. Ontologies have emerged in AI as a key tool to formally represent and semantically organize aspects of the real world. Beyond glossaries or thesauri, ontologies facilitate communication between experts and allow the application of computational techniques to extract useful information from available data. In medicinal chemistry, multiple ontologies have been developed during the last years which contain knowledge about chemical compounds and processes of synthesis of pharmaceutical products. This article reviews the principal standards and ontologies in medicinal chemistry, analyzes their main applications and suggests future directions.

  6. An Ontology-Driven Dependable Water Treatment Plant CPS

    Directory of Open Access Journals (Sweden)

    SANISLAV Teodora

    2013-05-01

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

  7. OWL 2 Web Ontology Language: XML serialization

    NARCIS (Netherlands)

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

    2008-01-01

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

  8. 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...

  9. A cognitive science perspective on legal ontologies

    NARCIS (Netherlands)

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

    2011-01-01

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

  10. Using Ontology Fingerprints to evaluate genome-wide association study results

    OpenAIRE

    Tsoi, Lam C.; Michael Boehnke; Klein, Richard L.; Jim Zheng, W.

    2009-01-01

    We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach...

  11. Ontology-Oriented Programming for Biomedical Informatics.

    Science.gov (United States)

    Lamy, Jean-Baptiste

    2016-01-01

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

  12. The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.

    Science.gov (United States)

    Lin, Yu; He, Yongqun

    2014-01-01

    Study 2. These results validated the proper OGSF structure identified different ontology aspects with SNA methods. OGSF provides a verified and robust framework for representing various genetic susceptibility types and genetic susceptibility factors annotated from experimental VAE genetic association studies. The RDF/OWL formulated ontology data can be queried using SPARQL and analyzed using centrality-based network analysis methods.

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

    Directory of Open Access Journals (Sweden)

    Phillip Lord

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

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

    Science.gov (United States)

    Hartung, Michael; Groß, Anika; Rahm, Erhard

    2013-02-01

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

  15. Archetypal TRMM Radar Profiles Identified Through Cluster Analysis

    Science.gov (United States)

    Boccippio, Dennis J.

    2003-01-01

    It is widely held that identifiable 'convective regimes' exist in nature, although precise definitions of these are elusive. Examples include land / Ocean distinctions, break / monsoon beahvior, seasonal differences in the Amazon (SON vs DJF), etc. These regimes are often described by differences in the realized local convective spectra, and measured by various metrics of convective intensity, depth, areal coverage and rainfall amount. Objective regime identification may be valuable in several ways: regimes may serve as natural 'branch points' in satellite retrieval algorithms or data assimilation efforts; one example might be objective identification of regions that 'should' share a similar 2-R relationship. Similarly, objectively defined regimes may provide guidance on optimal siting of ground validation efforts. Objectively defined regimes could also serve as natural (rather than arbitrary geographic) domain 'controls' in studies of convective response to environmental forcing. Quantification of convective vertical structure has traditionally involved parametric study of prescribed quantities thought to be important to convective dynamics: maximum radar reflectivity, cloud top height, 30-35 dBZ echo top height, rain rate, etc. Individually, these parameters are somewhat deficient as their interpretation is often nonunique (the same metric value may signify different physics in different storm realizations). Individual metrics also fail to capture the coherence and interrelationships between vertical levels available in full 3-D radar datasets. An alternative approach is discovery of natural partitions of vertical structure in a globally representative dataset, or 'archetypal' reflectivity profiles. In this study, this is accomplished through cluster analysis of a very large sample (0[107) of TRMM-PR reflectivity columns. Once achieved, the rainconditional and unconditional 'mix' of archetypal profile types in a given location and/or season provides a description

  16. Cluster Analysis of Clinical Data Identifies Fibromyalgia Subgroups

    Science.gov (United States)

    Docampo, Elisa; Collado, Antonio; Escaramís, Geòrgia; Carbonell, Jordi; Rivera, Javier; Vidal, Javier; Alegre, José

    2013-01-01

    Introduction Fibromyalgia (FM) is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. Material and Methods 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. Results Variables clustered into three independent dimensions: “symptomatology”, “comorbidities” and “clinical scales”. Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1), high symptomatology and comorbidities (Cluster 2), and high symptomatology but low comorbidities (Cluster 3), showing differences in measures of disease severity. Conclusions We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment. PMID:24098674

  17. Archetypal TRMM Radar Profiles Identified Through Cluster Analysis

    Science.gov (United States)

    Boccippio, Dennis J.

    2003-01-01

    It is widely held that identifiable 'convective regimes' exist in nature, although precise definitions of these are elusive. Examples include land / Ocean distinctions, break / monsoon beahvior, seasonal differences in the Amazon (SON vs DJF), etc. These regimes are often described by differences in the realized local convective spectra, and measured by various metrics of convective intensity, depth, areal coverage and rainfall amount. Objective regime identification may be valuable in several ways: regimes may serve as natural 'branch points' in satellite retrieval algorithms or data assimilation efforts; one example might be objective identification of regions that 'should' share a similar 2-R relationship. Similarly, objectively defined regimes may provide guidance on optimal siting of ground validation efforts. Objectively defined regimes could also serve as natural (rather than arbitrary geographic) domain 'controls' in studies of convective response to environmental forcing. Quantification of convective vertical structure has traditionally involved parametric study of prescribed quantities thought to be important to convective dynamics: maximum radar reflectivity, cloud top height, 30-35 dBZ echo top height, rain rate, etc. Individually, these parameters are somewhat deficient as their interpretation is often nonunique (the same metric value may signify different physics in different storm realizations). Individual metrics also fail to capture the coherence and interrelationships between vertical levels available in full 3-D radar datasets. An alternative approach is discovery of natural partitions of vertical structure in a globally representative dataset, or 'archetypal' reflectivity profiles. In this study, this is accomplished through cluster analysis of a very large sample (0[107) of TRMM-PR reflectivity columns. Once achieved, the rainconditional and unconditional 'mix' of archetypal profile types in a given location and/or season provides a description

  18. Identifying avian sources of faecal contamination using sterol analysis.

    Science.gov (United States)

    Devane, Megan L; Wood, David; Chappell, Andrew; Robson, Beth; Webster-Brown, Jenny; Gilpin, Brent J

    2015-10-01

    Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

  19. Network Analysis Identifies Disease-Specific Pathways for Parkinson's Disease.

    Science.gov (United States)

    Monti, Chiara; Colugnat, Ilaria; Lopiano, Leonardo; Chiò, Adriano; Alberio, Tiziana

    2016-12-21

    Neurodegenerative diseases are characterized by the progressive loss of specific neurons in selected regions of the central nervous system. The main clinical manifestation (movement disorders, cognitive impairment, and/or psychiatric disturbances) depends on the neuron population being primarily affected. Parkinson's disease is a common movement disorder, whose etiology remains mostly unknown. Progressive loss of dopaminergic neurons in the substantia nigra causes an impairment of the motor control. Some of the pathogenetic mechanisms causing the progressive deterioration of these neurons are not specific for Parkinson's disease but are shared by other neurodegenerative diseases, like Alzheimer's disease and amyotrophic lateral sclerosis. Here, we performed a meta-analysis of the literature of all the quantitative proteomic investigations of neuronal alterations in different models of Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis to distinguish between general and Parkinson's disease-specific pattern of neurodegeneration. Then, we merged proteomics data with genetics information from the DisGeNET database. The comparison of gene and protein information allowed us to identify 25 proteins involved uniquely in Parkinson's disease and we verified the alteration of one of them, i.e., transaldolase 1 (TALDO1), in the substantia nigra of 5 patients. By using open-source bioinformatics tools, we identified the biological processes specifically affected in Parkinson's disease, i.e., proteolysis, mitochondrion organization, and mitophagy. Eventually, we highlighted four cellular component complexes mostly involved in the pathogenesis: the proteasome complex, the protein phosphatase 2A, the chaperonins CCT complex, and the complex III of the respiratory chain.

  20. Social network analysis in identifying influential webloggers: A preliminary study

    Science.gov (United States)

    Hasmuni, Noraini; Sulaiman, Nor Intan Saniah; Zaibidi, Nerda Zura

    2014-12-01

    In recent years, second generation of internet-based services such as weblog has become an effective communication tool to publish information on the Web. Weblogs have unique characteristics that deserve users' attention. Some of webloggers have seen weblogs as appropriate medium to initiate and expand business. These webloggers or also known as direct profit-oriented webloggers (DPOWs) communicate and share knowledge with each other through social interaction. However, survivability is the main issue among DPOW. Frequent communication with influential webloggers is one of the way to keep survive as DPOW. This paper aims to understand the network structure and identify influential webloggers within the network. Proper understanding of the network structure can assist us in knowing how the information is exchanged among members and enhance survivability among DPOW. 30 DPOW were involved in this study. Degree centrality and betweenness centrality measurement in Social Network Analysis (SNA) were used to examine the strength relation and identify influential webloggers within the network. Thus, webloggers with the highest value of these measurements are considered as the most influential webloggers in the network.

  1. 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.

  2. On the ontology of the elementary particles. A philosophical analysis of the actual elementary-particle physics; Zur Ontologie der Elementarteilchen. Eine philosophische Analyse der aktuellen Elementarteilchenphysik

    Energy Technology Data Exchange (ETDEWEB)

    Brueckner, Thomas Christian

    2015-07-01

    After a description of the standard model of elementary-particle physics the author describes structuralistic reconstructions. Then the problem of the theoretical terms is discussed. Therafter the reconstruction of the standard-model elementary particles is described. Finally the ontology of leptons, quarks and both free and in atoms bound protons is considered.

  3. Use of the Protein Ontology (PRO for Multi-Faceted Analysis of Biological Processes: a Case Study of the Spindle Checkpoint

    Directory of Open Access Journals (Sweden)

    Karen E Ross

    2013-04-01

    Full Text Available As a member of the Open Biomedical Ontologies (OBO foundry, the Protein Ontology (PRO provides an ontological representation of protein forms and complexes and their relationships. Annotations in PRO can be assigned to individual protein forms and complexes, each distinguishable down to the level of post-translational modification, thereby allowing for a more precise depiction of protein function than is possible with annotations to the gene as a whole. Moreover, PRO is fully interoperable with other OBO ontologies and integrates knowledge from other protein-centric resources such as UniProt and Reactome. Here we demonstrate the value of the PRO framework in the investigation of the spindle checkpoint, a highly conserved biological process that relies extensively on protein modification and protein complex formation. The spindle checkpoint maintains genomic integrity by monitoring the attachment of chromosomes to spindle microtubules and delaying cell cycle progression until the spindle is fully assembled. Using PRO in conjunction with other bioinformatics tools, we explored the cross-species conservation of spindle checkpoint proteins, including phosphorylated forms and complexes; studied the impact of phosphorylation on spindle checkpoint function; and examined the interactions of spindle checkpoint proteins with the kinetochore, the site of checkpoint activation. Our approach can be generalized to any biological process of interest.

  4. A network-theoretic approach for decompositional translation across Open Biological Ontologies.

    Science.gov (United States)

    Patel, Chintan O; Cimino, James J

    2010-08-01

    Biological ontologies are now being widely used for annotation, sharing and retrieval of the biological data. Many of these ontologies are hosted under the umbrella of the Open Biological Ontologies Foundry. In order to support interterminology mapping, composite terms in these ontologies need to be translated into atomic or primitive terms in other, orthogonal ontologies, for example, gluconeogenesis (biological process term) to glucose (chemical ontology term). Identifying such decompositional ontology translations is a challenging problem. In this paper, we propose a network-theoretic approach based on the structure of the integrated OBO relationship graph. We use a network-theoretic measure, called the clustering coefficient, to find relevant atomic terms in the neighborhood of a composite term. By eliminating the existing GO to ChEBI Ontology mappings from OBO, we evaluate whether the proposed approach can re-identify the corresponding relationships. The results indicate that the network structure provides strong cues for decompositional ontology translation and the existing relationships can be used to identify new translations.

  5. 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

  6. Structure-based classification and ontology in chemistry.

    Science.gov (United States)

    Hastings, Janna; Magka, Despoina; Batchelor, Colin; Duan, Lian; Stevens, Robert; Ennis, Marcus; Steinbeck, Christoph

    2012-04-05

    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. 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. Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic

  7. OntoPIN: an ontology-annotated PPI database.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Veltri, Pierangelo; Cannataro, Mario

    2013-09-01

    Protein-protein interaction (PPI) data stored in publicly available databases are queried by the use of simple query interfaces allowing only key-based queries. A typical query on such databases is based on the use of protein identifiers and enables the retrieval of one or more proteins. Nevertheless, a lot of biological information is available and is spread on different sources and encoded in different ontologies such as Gene Ontology. The integration of existing PPI databases and biological information may result in richer querying interfaces and successively could enable the development of novel algorithms that may use biological information. The OntoPIN project showed the effectiveness of the introduction of a framework for the ontology-based management and querying of Protein-Protein Interaction Data. The OntoPIN framework first merges PPI data with annotations extracted from existing ontologies (e.g. Gene Ontology) and stores annotated data into a database. Then, a semantic-based query interface enables users to query these data by using biological concepts. OntoPIN allows: (a) to extend existing PPI databases by using ontologies, (b) to enable a key-based querying of annotated data, and (c) to offer a novel query interface based on semantic similarity among annotations.

  8. Ontology modularization to improve semantic medical image annotation.

    Science.gov (United States)

    Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul

    2011-02-01

    Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results.

  9. A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia.

    Science.gov (United States)

    Pérez-Santiago, Josué; Diez-Alarcia, Rebeca; Callado, Luis F; Zhang, Jin X; Chana, Gursharan; White, Cory H; Glatt, Stephen J; Tsuang, Ming T; Everall, Ian P; Meana, J Javier; Woelk, Christopher H

    2012-11-01

    Small cohort sizes and modest levels of gene expression changes in brain tissue have plagued the statistical approaches employed in microarray studies investigating the mechanism of schizophrenia. To combat these problems a combined analysis of six prior microarray studies was performed to facilitate the robust statistical analysis of gene expression data from the dorsolateral prefrontal cortex of 107 patients with schizophrenia and 118 healthy subjects. Multivariate permutation tests identified 144 genes that were differentially expressed between schizophrenia and control groups. Seventy of these genes were identified as differentially expressed in at least one component microarray study but none of these individual studies had the power to identify the remaining 74 genes, demonstrating the utility of a combined approach. Gene ontology terms and biological pathways that were significantly enriched for differentially expressed genes were related to neuronal cell-cell signaling, mesenchymal induction, and mitogen-activated protein kinase signaling, which have all previously been associated with the etiopathogenesis of schizophrenia. The differential expression of BAG3, C4B, EGR1, MT1X, NEUROD6, SST and S100A8 was confirmed by real-time quantitative PCR in an independent cohort using postmortem human prefrontal cortex samples. Comparison of gene expression between schizophrenic subjects with and without detectable levels of antipsychotics in their blood suggests that the modulation of MT1X and S100A8 may be the result of drug exposure. In conclusion, this combined analysis has resulted in a statistically robust identification of genes whose dysregulation may contribute to the mechanism of schizophrenia.

  10. Introducing defeasibility into OWL ontologies

    CSIR Research Space (South Africa)

    Casini, G

    2015-10-01

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

  11. Concept Approximation between Fuzzy Ontologies

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

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

  12. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

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

  13. Social ontologi og metodologisk individualisme

    DEFF Research Database (Denmark)

    Baldursson, Einar Baldvin

    2013-01-01

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

  14. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

    Science.gov (United States)

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

    2015-01-01

    Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using INO-based literature mining results, a modified Fisher's exact test was established to analyze significantly over- and under-represented enriched gene-gene interaction types within a specific area. Such a strategy was applied to study the vaccine-mediated gene-gene interactions using all PubMed abstracts. The Vaccine Ontology (VO) and INO were used to support the retrieval of vaccine terms and interaction keywords from the literature. INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies. Current INO includes 540 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms with 'INO_' prefix. A new annotation property, 'has literature mining keywords', was generated to allow the listing of different keywords mapping to the interaction types in INO. Using all PubMed documents published as of 12/31/2013, approximately 266,000 vaccine-associated documents were identified, and a total of 6,116 gene-pairs were associated with at least one INO term. Out of 78 INO interaction terms associated with at least five gene-pairs of the vaccine-associated sub-network, 14 terms were significantly over-represented (i.e., more frequently used) and 17 under-represented based on our modified Fisher's exact test. These over-represented and under-represented terms share some common top-level terms but are distinct at the bottom levels of the INO hierarchy. The analysis of these

  15. Musical Ontology: Critical, not Metaphysical

    Directory of Open Access Journals (Sweden)

    Jonathan A. Neufeld

    2014-01-01

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

  16. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    OpenAIRE

    Kirsten Toralf; Gross Anika; Hartung Michael; Rahm Erhard

    2011-01-01

    Abstract Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and ...

  17. A task-based approach for Gene Ontology evaluation.

    Science.gov (United States)

    Clarke, Erik L; Loguercio, Salvatore; Good, Benjamin M; Su, Andrew I

    2013-04-15

    The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact they have on gene set enrichment analysis, along with an example implementation. This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to the primary use of the annotations. Applied to specific areas of biological interest, our framework allowed us to understand the progress of annotation and structural ontology changes from 2004 to 2012. Our framework was also able to determine that the quality of annotations and structure in the area under test have been improving in their ability to recall underlying biological traits. Furthermore, we were able to distinguish between the impact of changes to the annotation sets and ontology structure. Our framework and implementation lay the groundwork for a powerful tool in evaluating the usefulness of the Gene Ontology. We demonstrate both the flexibility and the power of this approach in evaluating the current and past state of the Gene Ontology as well as its applicability in developing new methods for creating gene annotations.

  18. Knowledge Discovery from Biomedical Ontologies in Cross Domains.

    Science.gov (United States)

    Shen, Feichen; Lee, Yugyung

    2016-01-01

    In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies.

  19. Biomedical imaging ontologies: A survey and proposal for future work

    Science.gov (United States)

    Smith, Barry; Arabandi, Sivaram; Brochhausen, Mathias; Calhoun, Michael; Ciccarese, Paolo; Doyle, Scott; Gibaud, Bernard; Goldberg, Ilya; Kahn, Charles E.; Overton, James; Tomaszewski, John; Gurcan, Metin

    2015-01-01

    Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical definitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. PMID:26167381

  20. Knowledge Discovery from Biomedical Ontologies in Cross Domains

    Science.gov (United States)

    Shen, Feichen; Lee, Yugyung

    2016-01-01

    In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies. PMID:27548262

  1. Performance Analysis: Work Control Events Identified January - August 2010

    Energy Technology Data Exchange (ETDEWEB)

    De Grange, C E; Freeman, J W; Kerr, C E; Holman, G; Marsh, K; Beach, R

    2011-01-14

    This performance analysis evaluated 24 events that occurred at LLNL from January through August 2010. The analysis identified areas of potential work control process and/or implementation weaknesses and several common underlying causes. Human performance improvement and safety culture factors were part of the causal analysis of each event and were analyzed. The collective significance of all events in 2010, as measured by the occurrence reporting significance category and by the proportion of events that have been reported to the DOE ORPS under the ''management concerns'' reporting criteria, does not appear to have increased in 2010. The frequency of reporting in each of the significance categories has not changed in 2010 compared to the previous four years. There is no change indicating a trend in the significance category and there has been no increase in the proportion of occurrences reported in the higher significance category. Also, the frequency of events, 42 events reported through August 2010, is not greater than in previous years and is below the average of 63 occurrences per year at LLNL since 2006. Over the previous four years, an average of 43% of the LLNL's reported occurrences have been reported as either ''management concerns'' or ''near misses.'' In 2010, 29% of the occurrences have been reported as ''management concerns'' or ''near misses.'' This rate indicates that LLNL is now reporting fewer ''management concern'' and ''near miss'' occurrences compared to the previous four years. From 2008 to the present, LLNL senior management has undertaken a series of initiatives to strengthen the work planning and control system with the primary objective to improve worker safety. In 2008, the LLNL Deputy Director established the Work Control Integrated Project Team to develop the core requirements and graded

  2. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

    Directory of Open Access Journals (Sweden)

    Apweiler Rolf

    2006-02-01

    Full Text Available Abstract Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. Results The Ontology Lookup Service (OLS was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. Conclusion The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

  3. Identifying redundancy and exposing provenance in crowdsourced data analysis.

    Science.gov (United States)

    Willett, Wesley; Ginosar, Shiry; Steinitz, Avital; Hartmann, Björn; Agrawala, Maneesh

    2013-12-01

    We present a system that lets analysts use paid crowd workers to explore data sets and helps analysts interactively examine and build upon workers' insights. We take advantage of the fact that, for many types of data, independent crowd workers can readily perform basic analysis tasks like examining views and generating explanations for trends and patterns. However, workers operating in parallel can often generate redundant explanations. Moreover, because workers have different competencies and domain knowledge, some responses are likely to be more plausible than others. To efficiently utilize the crowd's work, analysts must be able to quickly identify and consolidate redundant responses and determine which explanations are the most plausible. In this paper, we demonstrate several crowd-assisted techniques to help analysts make better use of crowdsourced explanations: (1) We explore crowd-assisted strategies that utilize multiple workers to detect redundant explanations. We introduce color clustering with representative selection--a strategy in which multiple workers cluster explanations and we automatically select the most-representative result--and show that it generates clusterings that are as good as those produced by experts. (2) We capture explanation provenance by introducing highlighting tasks and capturing workers' browsing behavior via an embedded web browser, and refine that provenance information via source-review tasks. We expose this information in an explanation-management interface that allows analysts to interactively filter and sort responses, select the most plausible explanations, and decide which to explore further.

  4. A Sensitivity Analysis Approach to Identify Key Environmental Performance Factors

    Directory of Open Access Journals (Sweden)

    Xi Yu

    2014-01-01

    Full Text Available Life cycle assessment (LCA is widely used in design phase to reduce the product’s environmental impacts through the whole product life cycle (PLC during the last two decades. The traditional LCA is restricted to assessing the environmental impacts of a product and the results cannot reflect the effects of changes within the life cycle. In order to improve the quality of ecodesign, it is a growing need to develop an approach which can reflect the changes between the design parameters and product’s environmental impacts. A sensitivity analysis approach based on LCA and ecodesign is proposed in this paper. The key environmental performance factors which have significant influence on the products’ environmental impacts can be identified by analyzing the relationship between environmental impacts and the design parameters. Users without much environmental knowledge can use this approach to determine which design parameter should be first considered when (redesigning a product. A printed circuit board (PCB case study is conducted; eight design parameters are chosen to be analyzed by our approach. The result shows that the carbon dioxide emission during the PCB manufacture is highly sensitive to the area of PCB panel.

  5. Identifying covariates of population health using extreme bound analysis.

    Science.gov (United States)

    Carmignani, Fabrizio; Shankar, Sriram; Tan, Eng Joo; Tang, Kam Ki

    2014-06-01

    The literature is full of lively discussion on the determinants of population health outcomes. However, different papers focus on small and different sets of variables according to their research agenda. Because many of these variables are measures of different aspects of development and are thus correlated, the results for one variable can be sensitive to the inclusion/exclusion of others. We tested for the robustness of potential predictors of population health using the extreme bounds analysis. Population health was measured by life expectancy at birth and infant mortality rate. We found that only about half a dozen variables are robust predictors for life expectancy and infant mortality rate. Among them, adolescent fertility rate, improved water sources, and gender equality are the most robust. All institutional variables and environment variables are systematically non-robust predictors of population health. The results highlight the importance of robustness tests in identifying predictors or potential determinants of population health, and cast doubts on the findings of previous studies that fail to do so.

  6. Global secretome analysis identifies novel mediators of bone metastasis

    Institute of Scientific and Technical Information of China (English)

    Mario Andres Blanco; Gary LeRoy; Zia Khan; Ma(s)a Ale(c)kovi(c); Barry M Zee; Benjamin A Garcia; Yibin Kang

    2012-01-01

    Bone is the one of the most common sites of distant metastasis of solid tumors.Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma.To comprehensively profile secreted proteins associated with bone metastasis,we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types.By comparing the secretomes of parental cells and their bone metastatic derivatives,we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines.We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis.Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1,CST2,and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1.Overall,our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.

  7. Performance Analysis: Work Control Events Identified January - August 2010

    Energy Technology Data Exchange (ETDEWEB)

    De Grange, C E; Freeman, J W; Kerr, C E; Holman, G; Marsh, K; Beach, R

    2011-01-14

    This performance analysis evaluated 24 events that occurred at LLNL from January through August 2010. The analysis identified areas of potential work control process and/or implementation weaknesses and several common underlying causes. Human performance improvement and safety culture factors were part of the causal analysis of each event and were analyzed. The collective significance of all events in 2010, as measured by the occurrence reporting significance category and by the proportion of events that have been reported to the DOE ORPS under the ''management concerns'' reporting criteria, does not appear to have increased in 2010. The frequency of reporting in each of the significance categories has not changed in 2010 compared to the previous four years. There is no change indicating a trend in the significance category and there has been no increase in the proportion of occurrences reported in the higher significance category. Also, the frequency of events, 42 events reported through August 2010, is not greater than in previous years and is below the average of 63 occurrences per year at LLNL since 2006. Over the previous four years, an average of 43% of the LLNL's reported occurrences have been reported as either ''management concerns'' or ''near misses.'' In 2010, 29% of the occurrences have been reported as ''management concerns'' or ''near misses.'' This rate indicates that LLNL is now reporting fewer ''management concern'' and ''near miss'' occurrences compared to the previous four years. From 2008 to the present, LLNL senior management has undertaken a series of initiatives to strengthen the work planning and control system with the primary objective to improve worker safety. In 2008, the LLNL Deputy Director established the Work Control Integrated Project Team to develop the core requirements and graded

  8. Critical Theory and Processual Social Ontology

    Directory of Open Access Journals (Sweden)

    Renault Emmanuel

    2016-03-01

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

  9. GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

    Science.gov (United States)

    Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

    2010-02-01

    Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

  10. Automatic Learning of Ontologies for the Semantic Web: experiment lexical learning

    Directory of Open Access Journals (Sweden)

    Eduard Puerto

    2012-07-01

    Full Text Available This paper proposes the design of a System for Automatic Learning of Ontologies and Lexical Information (SALOX for the Dynamic Semantic Ontological Framework for the Semantic Web (DSOFSW. DSOFSW interprets query in natural language (Spanish to the web, and is composed by five parts; a linguistic ontology for the grammar of Spanish, a lexicon for the lexical information, a database of facts about the system experiences, a task ontology for the linguistic analysis process, and an interpretative ontology of the context. SALOX integrates several methods, approaches and techniques for information extraction, discovery and actualization (pragmatic (user profile, context knowledge, lexical and semantic linguistic information, etc. in order to update the knowledge used for DSOFSW. SALOX has a component to map the sources of learning with the learning methods, and another to update the linguistic ontology and the lexicon of the DSOFSW. Specifically, in this paper we present the design of the learning unit of lexical information.

  11. Measuring the evolution of ontology complexity: the gene ontology case study.

    Science.gov (United States)

    Dameron, Olivier; Bettembourg, Charles; Le Meur, Nolwenn

    2013-01-01

    Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches, i.e. biological processes (BP), cellular components (CC) and molecular functions (MF). For each case, we measured complexity by computing metrics related to the size, the nodes connectivity and the hierarchical structure. The number of classes and relations increased monotonously for each branch, with different growth rates. BP and CC had similar connectivity, superior to that of MF. Connectivity increased monotonously for BP, decreased for CC and remained stable for MF, with a marked increase for the three branches in November and December 2012. Hierarchy-related measures showed that CC and MF had similar proportions of leaves, average depths and average heights. BP had a lower proportion of leaves, and a higher average depth and average height. For BP and MF, the late 2012 increase of connectivity resulted in an increase of the average depth and average height and a decrease of the proportion of leaves, indicating that a major enrichment effort of the intermediate-level hierarchy occurred. The variation of the number of classes and relations in an ontology does not provide enough information about the evolution of its complexity. However, connectivity and hierarchy-related metrics revealed different patterns of values as well as of evolution for the three branches of the Gene Ontology. CC was similar to BP in terms of connectivity, and similar to MF in terms of hierarchy. Overall, BP complexity increased, CC was refined with the addition of leaves providing a finer level of annotations but decreasing slightly its complexity, and MF complexity remained stable.

  12. A framework for unifying ontology-based semantic similarity measures: a study in the biomedical domain.

    Science.gov (United States)

    Harispe, Sébastien; Sánchez, David; Ranwez, Sylvie; Janaqi, Stefan; Montmain, Jacky

    2014-04-01

    Ontologies are widely adopted in the biomedical domain to characterize various resources (e.g. diseases, drugs, scientific publications) with non-ambiguous meanings. By exploiting the structured knowledge that ontologies provide, a plethora of ad hoc and domain-specific semantic similarity measures have been defined over the last years. Nevertheless, some critical questions remain: which measure should be defined/chosen for a concrete application? Are some of the, a priori different, measures indeed equivalent? In order to bring some light to these questions, we perform an in-depth analysis of existing ontology-based measures to identify the core elements of semantic similarity assessment. As a result, this paper presents a unifying framework that aims to improve the understanding of semantic measures, to highlight their equivalences and to propose bridges between their theoretical bases. By demonstrating that groups of measures are just particular instantiations of parameterized functions, we unify a large number of state-of-the-art semantic similarity measures through common expressions. The application of the proposed framework and its practical usefulness is underlined by an empirical analysis of hundreds of semantic measures in a biomedical context. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. The ultimate constituents of the material world in search of an ontology for fundamental physics

    CERN Document Server

    Kuhlmann, Meinard

    2010-01-01

    Today, quantum field theory (QFT)-the mathematical and conceptual framework for contemporary elementary particle physics-is the best starting point for analysing the fundamental building blocks of the material world. QFT if taken seriously in its metaphysical implications yields a picture of the world that is at variance with central classical conceptions. The core of Kuhlmann's investigation consists in the analysis of various ontological interpretations of QFT, e.g. substance ontologies as well as a process-ontological approach. Eventually, Kuhlmann proposes a dispositional trope ontology, a

  14. Identifying Phytoplankton Classes In California Reservoirs Using HPLC Pigment Analysis

    Science.gov (United States)

    Siddiqui, S.; Peacock, M. B.; Kudela, R. M.; Negrey, K.

    2014-12-01

    Few bodies of water are routinely monitored for phytoplankton composition due to monetary and time constraints, especially the less accessible bodies of water in central and southern California. These lakes and estuaries are important for economic reasons such as tourism and fishing. This project investigated the composition of phytoplankton present using pigment analysis to identify dominant phytoplankton groups. A total of 28 different sites with a wide range of salinity (0 - 60) in central and southern California were examined. These included 13 different bodies of water in central California: 6 in the Sierras, 7 in the San Francisco Bay Estuary, and 15 from southern California. The samples were analyzed using high-performance liquid-chromatography (HPLC) to quantify the pigments present (using retention time and the spectral thumbprint). Diagnostic pigments were used to indicate the phytoplankton class composition, focusing on diatoms, dinoflagellates, cryptophytes, and cyanobacteria - all key phytoplankton groups indicative of the health of the sampled reservoir. Our results indicated that cyanobacteria dominated four of the seven bodies of central California water (Mono Lake, Bridgeport Reservoir, Steamboat Slough, and Pinto Lake); cryptophytes and nannoflagellates dominated two of the central California bodies of water (Mare Island Strait and Topaz Lake); and diatoms and dinoflagellates dominated one central California body of water, Oakland Inner Harbor, comprising more than 70% of the phytoplankton present. We expect the bodies of water from Southern California to be as disparate. Though this data is only a snapshot, it has significant implications in comparing different ecosystems across California, and it has the potential to provide valuable insight into the composition of phytoplankton communities.

  15. Historical and Conceptual Foundation of Diagrammatical Ontology

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Uckelman, Sara L.; Schärfe, Henrik

    2007-01-01

    During the Renaissance there was a growing interest for the use of diagrams within conceptual studies. This paper investigates the historical and philosophical foundation of this renewed use of diagrams in ontology as well as the modern relevance of this foundation. We discuss the historical...... and philosophical background for Jacob Lorhard’s invention of the word ‘ontology’ as well as the scientific status of ontology in the 16th and 17th century. We also consider the use of Ramean style diagrams and diagrammatic ontology in general. A modern implementation of Lorhard’s ontology is discussed...... and this classical ontology is compared to some modern ontologies....

  16. Historical and Conceptual Foundation of Diagrammatical Ontology

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Uckelman, Sara L.; Schärfe, Henrik

    2007-01-01

    During the Renaissance there was a growing interest for the use of diagrams within conceptual studies. This paper investigates the historical and philosophical foundation of this renewed use of diagrams in ontology as well as the modern relevance of this foundation. We discuss the historical...... and philosophical background for Jacob Lorhard’s invention of the word ‘ontology’ as well as the scientific status of ontology in the 16th and 17th century. We also consider the use of Ramean style diagrams and diagrammatic ontology in general. A modern implementation of Lorhard’s ontology is discussed...... and this classical ontology is compared to some modern ontologies....

  17. Cohesion Metrics for Ontology Design and Application

    Directory of Open Access Journals (Sweden)

    Haining Yao

    2005-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ali Ahmed

    2014-04-01

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

  19. Knowledge resources fuzzy clustering analysis based on ontology%基于本体的知识资源模糊聚类分析

    Institute of Scientific and Technical Information of China (English)

    李广明

    2011-01-01

    This paper proposed an ontology-based knowledge resources fuzzy clustering method, through decomposed ontology, calculated element space vector, calculated the semantic distance between knowledge ontology to express fuzzy similarity,at last, to process fuzzy clustering. Finally proposed examples which demonstrated the method.%针对知识资源分块的边界模糊性的特点,以知识资源的本体表示为基础,应用基于本体的知识资源模糊聚类方法,通过分解知识本体,计算概念、属性、关系、结构等知识构成元素的空间向量,结合WordNet的词汇映射关系,使用知识本体间的语义距离表示知识资源间的模糊相似度,来实现知识本体的模糊聚类.最后举出实例来描述本文应用的方法,说明模糊聚类方法可以较好地分类知识资源.

  20. Advancing science through mining libraries, ontologies, and communities.

    Science.gov (United States)

    Evans, James A; Rzhetsky, Andrey

    2011-07-08

    Life scientists today cannot hope to read everything relevant to their research. Emerging text-mining tools can help by identifying topics and distilling statements from books and articles with increased accuracy. Researchers often organize these statements into ontologies, consistent systems of reality claims. Like scientific thinking and interchange, however, text-mined information (even when accurately captured) is complex, redundant, sometimes incoherent, and often contradictory: it is rooted in a mixture of only partially consistent ontologies. We review work that models scientific reason and suggest how computational reasoning across ontologies and the broader distribution of textual statements can assess the certainty of statements and the process by which statements become certain. With the emergence of digitized data regarding networks of scientific authorship, institutions, and resources, we explore the possibility of accounting for social dependences and cultural biases in reasoning models. Computational reasoning is starting to fill out ontologies and flag internal inconsistencies in several areas of bioscience. In the not too distant future, scientists may be able to use statements and rich models of the processes that produced them to identify underexplored areas, resurrect forgotten findings and ideas, deconvolute the spaghetti of underlying ontologies, and synthesize novel knowledge and hypotheses.

  1. 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

  2. An Analysis of Service Ontologies

    NARCIS (Netherlands)

    Sorathia, Vikram; Ferreira Pires, Luis; Sinderen, van Marten

    2010-01-01

    Services are increasingly shaping the world’s economic activity. Service provision and consumption have been profiting from advances in ICT, but the decentralization and heterogeneity of the involved service entities still pose engineering challenges. One of these challenges is to achieve semantic i

  3. Tutorial on Protein Ontology Resources.

    Science.gov (United States)

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

    2017-01-01

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

  4. Ontologies and Formation Spaces for Conceptual ReDesign of Systems

    Directory of Open Access Journals (Sweden)

    J. Bíla

    2005-01-01

    Full Text Available This paper discusses ontologies, methods for developing them and languages for representing them. A special ontology for computational support of the Conceptual ReDesign Process (CRDP is introduced with a simple illustrative example of an application. The ontology denoted as Global context (GLB combines features of general semantic networks and features of UML language. The ontology is task-oriented and domain-oriented, and contains three basic strata – GLBExpl(stratum of Explanation, GLBFAct (stratum of Fields of Activities and GLBEnv (stratum of Environment, with their sub-strata. The ontology has been developed to represent functions of systems and their components in CRDP. The main difference between this ontology and ontologies which have been developed to identify functions (the semantic details in those ontologies must be as deep as possible is in the style of the description of the functions. In the proposed ontology, Formation Spaces were used as lower semantic categories the semantic deepness of which is variable and depends on the actual solution approach of a specialised Conceptual Designer.

  5. A family-based framework for supporting quality assurance of biomedical ontologies in BioPortal.

    Science.gov (United States)

    He, Zhe; Ochs, Christopher; Agrawal, Ankur; Perl, Yehoshua; Zeginis, Dimitris; Tarabanis, Konstantinos; Elhanan, Gai; Halper, Michael; Noy, Natasha; Geller, James

    2013-01-01

    BioPortal contains over 300 ontologies, for which quality assurance (QA) is critical. Abstraction networks (ANs), compact summarizations of ontology structure and content, have been used in such QA efforts, typically in a "one-off" manner for a single ontology. Ontologies can be characterized-independently of knowledge-content focus-from a structural standpoint leading to the formulation of ontology families. A family is defined as a set of ontologies satisfying some overarching condition regarding their structural features. Seven such families, comprising 186 ontologies, are identified. To increase efficiency, a new family-based QA framework is introduced in which an automated, uniform AN derivation technique and accompanying semi-automated, uniform QA regimen are applicable to the ontologies of a given family. Specifically, across an entire family, the QA efforts exploit family-wide AN features in the characterization of sets of classes that are more likely to harbor errors. The approach is demonstrated on the Cancer Chemoprevention BioPortal ontology.

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

    Directory of Open Access Journals (Sweden)

    G. M. Korotenko

    2017-08-01

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

  7. Identifying Ecosystem Services of Rivers and Streams Through Content Analysis

    Science.gov (United States)

    While much ecosystem services research focuses on analysis such as mapping and/or valuation, fewer research efforts are directed toward in-depth understanding of the specific ecological quantities people value. Ecosystem service monitoring and analysis efforts and communications ...

  8. 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...

  9. Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.

    Science.gov (United States)

    Bowles, Neil E; Jou, Chuanchau J; Arrington, Cammon B; Kennedy, Brett J; Earl, Aubree; Matsunami, Norisada; Meyers, Lindsay L; Etheridge, Susan P; Saarel, Elizabeth V; Bleyl, Steven B; Yost, H Joseph; Yandell, Mark; Leppert, Mark F; Tristani-Firouzi, Martin; Gruber, Peter J

    2015-12-01

    Wolff-Parkinson-White (WPW) syndrome is a common cause of supraventricular tachycardia that carries a risk of sudden cardiac death. To date, mutations in only one gene, PRKAG2, which encodes the 5'-AMP-activated protein kinase subunit γ-2, have been identified as causative for WPW. DNA samples from five members of a family with WPW were analyzed by exome sequencing. We applied recently designed prioritization strategies (VAAST/pedigree VAAST) coupled with an ontology-based algorithm (Phevor) that reduced the number of potentially damaging variants to 10: a variant in KCNE2 previously associated with Long QT syndrome was also identified. Of these 11 variants, only MYH6 p.E1885K segregated with the WPW phenotype in all affected individuals and was absent in 10 unaffected family members. This variant was predicted to be damaging by in silico methods and is not present in the 1,000 genome and NHLBI exome sequencing project databases. Screening of a replication cohort of 47 unrelated WPW patients did not identify other likely causative variants in PRKAG2 or MYH6. MYH6 variants have been identified in patients with atrial septal defects, cardiomyopathies, and sick sinus syndrome. Our data highlight the pleiotropic nature of phenotypes associated with defects in this gene.

  10. 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.

  11. On the ontology of spacetime

    CERN Document Server

    Romero, Gustavo E

    2015-01-01

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

  12. A Statistical Amalgamation Approach for Ontologies

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2012-02-01

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

  13. Research on Forging Die Design Ontology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenlei; FAN Yushun

    2006-01-01

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

  14. 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...

  15. Fregego krytyka dowodu ontologicznego (FREGE'S CRITICISM OF THE ONTOLOGICAL ARGUMENT

    Directory of Open Access Journals (Sweden)

    Arkadiusz Gut

    2005-06-01

    Full Text Available The paper reconstructs Frege's criticism of the ontological argument for the existence of God on the basis of various remarks scattered in his writings. The material is organized in such a way as to: (a reveal a logical structure of the argument; (b show and discern various presupposition of a logical, semantical and ontological character; and (c indicate some essential weaknesses of the ontological argument. It is argued that Frege's critical commentaries on this argument are essentially connected to four solutions, stating that: (1 the difference between a name and a predicate is categorical; (2 the existential judgement possesses a different logical structure than the singular judgement; (3 in the characteristic of concepts marks and properties should be distinguished; (4 the ascription of number contains the statement about a concept. In order to make Frege's argumentation as understandable as possible it is confronted with Kant's criticism of ontological argument. The analysis carried on in the above-described way reveals a number of shortcomings which discredit the ontological argument. For example, the paper shows that the analysis of predication of oneness (Einzigkeit does not lead to the affirmation of God's existence. Moreover, it shows that in that argument the term God is used in two different semantic roles; that some theses that should constitute the argument's conclusion, are already assumed; and that sense-condition and truth-conditions are not distinguished.Other author's publications:

  16. Towards a Consistent and Scientifically Accurate Drug Ontology.

    Science.gov (United States)

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

    2013-01-01

    Our use case for comparative effectiveness research requires an ontology of drugs that enables querying National Drug Codes (NDCs) by active ingredient, mechanism of action, physiological effect, and therapeutic class of the drug products they represent. We conducted an ontological analysis of drugs from the realist perspective, and evaluated existing drug terminology, ontology, and database artifacts from (1) the technical perspective, (2) the perspective of pharmacology and medical science (3) the perspective of description logic semantics (if they were available in Web Ontology Language or OWL), and (4) the perspective of our realism-based analysis of the domain. No existing resource was sufficient. Therefore, we built the Drug Ontology (DrOn) in OWL, which we populated with NDCs and other classes from RxNorm using only content created by the National Library of Medicine. We also built an application that uses DrOn to query for NDCs as outlined above, available at: http://ingarden.uams.edu/ingredients. The application uses an OWL-based description logic reasoner to execute end-user queries. DrOn is available at http://code.google.com/p/dr-on.

  17. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    2013-01-01

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

  18. Building an ontology for cyberterrorism

    CSIR Research Space (South Africa)

    Veerasamy, N

    2012-07-01

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

  19. 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

  20. 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...

  1. 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

  2. A Customizable Language Learning Support System Using Ontology-Driven Engine

    Science.gov (United States)

    Wang, Jingyun; Mendori, Takahiko; Xiong, Juan

    2013-01-01

    This paper proposes a framework for web-based language learning support systems designed to provide customizable pedagogical procedures based on the analysis of characteristics of both learner and course. This framework employs a course-centered ontology and a teaching method ontology as the foundation for the student model, which includes learner…

  3. A Customizable Language Learning Support System Using Ontology-Driven Engine

    Science.gov (United States)

    Wang, Jingyun; Mendori, Takahiko; Xiong, Juan

    2013-01-01

    This paper proposes a framework for web-based language learning support systems designed to provide customizable pedagogical procedures based on the analysis of characteristics of both learner and course. This framework employs a course-centered ontology and a teaching method ontology as the foundation for the student model, which includes learner…

  4. Ontology Matching for Big Data Applications in the Smart Dairy Farming Domain.

    NARCIS (Netherlands)

    Verhoosel, J.P.C.; Bekkum, M.A. van; Evert, F.K. van

    2015-01-01

    This paper addresses the use of ontologies for combining different sensor data sources to enable big data analysis in the dairy farming domain. We have made existing data sources accessible via linked data RDF mechanisms using OWL ontologies on Virtuoso and D2RQ triple stores. In addition, we have c

  5. Ontology Matching for Big Data Applications in the Smart Dairy Farming Domain.

    NARCIS (Netherlands)

    Verhoosel, J.P.C.; Bekkum, M.A. van; Evert, F.K. van

    2015-01-01

    This paper addresses the use of ontologies for combining different sensor data sources to enable big data analysis in the dairy farming domain. We have made existing data sources accessible via linked data RDF mechanisms using OWL ontologies on Virtuoso and D2RQ triple stores. In addition, we have c

  6. Ontology-driven health information systems architectures.

    Science.gov (United States)

    Blobel, Bernd; Oemig, Frank

    2009-01-01

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

  7. Ontology Translation: The Semiotic Engineering of Content Management Systems

    Directory of Open Access Journals (Sweden)

    Alejandro Villamarin M.

    2015-12-01

    Full Text Available The present paper proposes the application of Semiotic Engineering theory to Content Management Systems (CMS focusing on the analysis of how the use of different ontologies can affect the user’s efficiency when performing tasks in a CMS. The analysis is performed using the theoretical semiotic model Web-Semiotic Interface Design Evaluation (W-SIDE model.

  8. Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.

    Science.gov (United States)

    Qin, Tingting; Matmati, Nabil; Tsoi, Lam C; Mohanty, Bidyut K; Gao, Nan; Tang, Jijun; Lawson, Andrew B; Hannun, Yusuf A; Zheng, W Jim

    2014-10-01

    To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise comparison of all yeast genes' Ontology Fingerprints--a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene along with those terms' corresponding enrichment P-values. The network was further refined using a Bayesian hierarchical model to identify novel genes that could potentially influence the pathway activities. We applied this method to the sphingolipid pathway in yeast and found that many top-ranked genes indeed displayed altered sphingolipid pathway functions, initially measured by their sensitivity to myriocin, an inhibitor of de novo sphingolipid biosynthesis. Further experiments confirmed the modulation of the sphingolipid pathway by one of these genes, PFA4, encoding a palmitoyl transferase. Comparative analysis showed that few of these novel genes could be discovered by other existing methods. Our novel gene network provides a unique and comprehensive resource to study pathway modulations and systems biology in general. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Directory of Open Access Journals (Sweden)

    Claudia Villalonga

    2016-09-01

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

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

    CERN Document Server

    Lange, Christoph; Mossakowski, Till; Grüninger, Michael

    2012-01-01

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

  11. Identifying subgroups of patients using latent class analysis

    DEFF Research Database (Denmark)

    Nielsen, Anne Mølgaard; Kent, Peter; Hestbæk, Lise

    2017-01-01

    (activity, contextual factors, pain, participation, physical impairment and psychology) (first stage) as the variables entered into the second stage of the two-stage LCA to identify patient subgroups. The description of the results of the single-stage and two-stage LCA was based on a combination...... identified similar, but not identical, patient subgroups characterised by (i) mild intermittent LBP, (ii) recent severe LBP and activity limitations, (iii) very recent severe LBP with both activity and participation limitations, (iv) work-related LBP, (v) LBP and several negative consequences and (vi) LBP...

  12. Quality assurance of the gene ontology using abstraction networks.

    Science.gov (United States)

    Ochs, Christopher; Perl, Yehoshua; Halper, Michael; Geller, James; Lomax, Jane

    2016-06-01

    The gene ontology (GO) is used extensively in the field of genomics. Like other large and complex ontologies, quality assurance (QA) efforts for GO's content can be laborious and time consuming. Abstraction networks (AbNs) are summarization networks that reveal and highlight high-level structural and hierarchical aggregation patterns in an ontology. They have been shown to successfully support QA work in the context of various ontologies. Two kinds of AbNs, called the area taxonomy and the partial-area taxonomy, are developed for GO hierarchies and derived specifically for the biological process (BP) hierarchy. Within this framework, several QA heuristics, based on the identification of groups of anomalous terms which exhibit certain taxonomy-defined characteristics, are introduced. Such groups are expected to have higher error rates when compared to other terms. Thus, by focusing QA efforts on anomalous terms one would expect to find relatively more erroneous content. By automatically identifying these potential problem areas within an ontology, time and effort will be saved during manual reviews of GO's content. BP is used as a testbed, with samples of three kinds of anomalous BP terms chosen for a taxonomy-based QA review. Additional heuristics for QA are demonstrated. From the results of this QA effort, it is observed that different kinds of inconsistencies in the modeling of GO can be exposed with the use of the proposed heuristics. For comparison, the results of QA work on a sample of terms chosen from GO's general population are presented.

  13. INTELLIGENT INFORMATION RETRIEVAL WITHIN DIGITAL LIBRARY USING DOMAIN ONTOLOGY

    Directory of Open Access Journals (Sweden)

    Thinn Mya Mya Swe

    2011-07-01

    Full Text Available A digital library is a type of information retrieval (IR system. The existing information retrieval methodologies generally have problems on keyword-searching. We proposed a model to solve the problem by using concept-based approach (ontology and metadata case base. This model consists of identifying domain concepts in user’s query and applying expansion to them. The system aims at contributing to an improved relevance of results retrieved from digital libraries by proposing a conceptual query expansion for intelligent concept-based retrieval. We need to import the concept of ontology, making use of its advantage of abundant semantics and standard concept. Domain specific ontology can be used to improve information retrieval from traditional level based on keyword to the lay based on knowledge (or concept and change the process of retrieval from traditional keyword matching to semantics matching. One approach is query expansion techniques using domain ontology and the other would be introducing a case based similarity measure for metadata information retrieval using Case Based Reasoning (CBR approach. Results show improvements over classic method, query expansion using general purpose ontology and a number of other approaches.

  14. Use of Photogrammetry and Biomechanical Gait analysis to Identify Individuals

    DEFF Research Database (Denmark)

    Larsen, Peter Kastmand; Simonsen, Erik Bruun; Lynnerup, Niels

    Photogrammetry and recognition of gait patterns are valuable tools to help identify perpetrators based on surveillance recordings. We have found that stature but only few other measures have a satisfying reproducibility for use in forensics. Several gait variables with high recognition rates were...

  15. Similarity transformation approach to identifiability analysis of nonlinear compartmental models.

    Science.gov (United States)

    Vajda, S; Godfrey, K R; Rabitz, H

    1989-04-01

    Through use of the local state isomorphism theorem instead of the algebraic equivalence theorem of linear systems theory, the similarity transformation approach is extended to nonlinear models, resulting in finitely verifiable sufficient and necessary conditions for global and local identifiability. The approach requires testing of certain controllability and observability conditions, but in many practical examples these conditions prove very easy to verify. In principle the method also involves nonlinear state variable transformations, but in all of the examples presented in the paper the transformations turn out to be linear. The method is applied to an unidentifiable nonlinear model and a locally identifiable nonlinear model, and these are the first nonlinear models other than bilinear models where the reason for lack of global identifiability is nontrivial. The method is also applied to two models with Michaelis-Menten elimination kinetics, both of considerable importance in pharmacokinetics, and for both of which the complicated nature of the algebraic equations arising from the Taylor series approach has hitherto defeated attempts to establish identifiability results for specific input functions.

  16. Identifying failure mechanisms in LDMOS transistors by analytical stability analysis

    NARCIS (Netherlands)

    Ferrara, A.; Steeneken, P.G.; Boksteen, B.K.; Heringa, A.; Scholten, A.J.; Schmitz, J.; Hueting, R.J.E.

    2014-01-01

    In this work, analytical stability equations are derived and combined with a physics-based model of an LDMOS transistor in order to identify the primary cause of failure in different operating and bias conditions. It is found that there is a gradual boundary between an electrical failure region at h

  17. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

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

    2007-01-01

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

  18. Aspects of ontology visualization and integration

    NARCIS (Netherlands)

    Dmitrieva, Joelia Borisovna

    2011-01-01

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

  19. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

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

    2007-01-01

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

  20. Aspects of ontology visualization and integration

    NARCIS (Netherlands)

    Dmitrieva, Joelia Borisovna

    2011-01-01

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