Bioinformatics Commons^™

Integrating Semantic Web Services For Mobile Access, Anupriya Ankolekar, Pascal Hitzler, Holger Lewen, Daniel Oberle, Rudi Studer

Computer Science and Engineering Faculty Publications

We present our work in integrating Semantic Web services for access via mobile devices. We have developed a system, the WebServiceAccessComponent, that transforms a user request for a service on a mobile device, to a Web service request and then selects a matching service from the existing Web services of the Deutsche Telekom, which provide navigational and weather information. In this poster, we present the requirements and design of the WebServiceAccessComponent.

Cgkb-Cyanogroup Genomics Knowledge Base, Tin-Chun Chu, Lee Lee, Shankar Srinivasan, John Gaynor, Quinn Vega, Bonnie Lustigman

Tin-Chun Chu, Ph.D.

No abstract provided.

New Statistical Paradigms Leading To Web-Based Tools For Clinical/Translational Science, Knut M. Wittkowski

COBRA Preprint Series

As the field of functional genetics and genomics is beginning to mature, we become confronted with new challenges. The constant drop in price for sequencing and gene expression profiling as well as the increasing number of genetic and genomic variables that can be measured makes it feasible to address more complex questions. The success with rare diseases caused by single loci or genes has provided us with a proof-of-concept that new therapies can be developed based on functional genomics and genetics.

Common diseases, however, typically involve genetic epistasis, genomic pathways, and proteomic pattern. Moreover, to better understand the underlying biologi-cal …

An Ontological Approach To The Document Access Problem Of Insider Threat, Boanerges Aleman-Meza, Phillip Burns, Matthew Eavenson, Devanand Palanswami, Amit P. Sheth

Kno.e.sis Publications

Verification of legitimate access of documents, which is one aspect of the umbrella of problems in the Insider Threat category, is a challenging problem. This paper describes the research and prototyping of a system that takes an ontological approach, and is primarily targeted for use by theintelligence community. Our approach utilizes the notion of semantic associations and their discovery among a collection of heterogeneous documents. We highlight our contributions in (graphically) capturing the scope of the investigation assignment of an intelligence analyst by referring to classes and relationships of an ontology; in computing a measure of the relevance …

Semantic Web Services For N-Glycosylation Process, Satya S. Sahoo, Amit P. Sheth, William S. York, John A. Miller

Kno.e.sis Publications

Glycomics is one of the many research efforts currently underway in the biosciences domain, which is characterized by high throughput data generated at multiple experimental stages. For example, analysis of N-glycosylation encompasses stages from cell-culture to peptide identification and quantification. Research groups across the world use diverse cell cultures, separation and spectroscopic techniques, and data identification, correlation and integration methodologies. Thus, data generated at different phases of the process by multiple groups are both structurally and functionally heterogeneous.

Web Services To Semantic Web Processes: Investigating Synergy Between Practice And Research, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Bridging The Paradigm Gap With Rules For Owl, Jurgen Angele, Boris Motik, Rudi Studer, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Accelerated by the vision of the semantic web, semantic technologies have recently made significant advances. The underlying methods and paradigms are already being transferred to adjacent areas of research in artificial intelligence, knowledge management, and elsewhere. Textbooks explaining the foundations have appeared. Large national and international projects on the topic are under way.

Web Service Semantics - Wsdl-S, Rama Akkiraju, Joel Farrell, John A. Miller, Meenakshi Nagarajan, Amit P. Sheth, Kunal Verma

Kno.e.sis Publications

The current WSDL standard operates at the syntactic level and lacks the semantic expressivity needed to represent the requirements and capabilities of Web Services. Semantics can improve software reuse and discovery, significantly facilitate composition of Web services and enable integrating legacy applications as part of business process integration. The Web Service Semantic s technical note defines a mechanism to associate semantic annotations with Web services that are described using Web Service Description Language (WSDL). It is conceptually based on, but a significant refinement in details of, the original WSDL-S proposal [WSDL-S] from the LSDIS laboratory at the University of Georgia. …

Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

An Information Extraction Approach To Reorganizing And Summarizing Specifications, Krishnaprasad Thirunarayan, Aaron Berkovich, Dan Z. Sokol

Kno.e.sis Publications

Materials and Process Specifications are complex semi-structured documents containing numeric data, text, and images. This article describes a coarse-grain extraction technique to automatically reorganize and summarize spec content. Specifically, a strategy for semantic-markup, to capture content within a semantic ontology, relevant to semi-automatic extraction, has been developed and experimented with. The working prototypes were built in the context of Cohesia's existing software infrastructure, and use techniques from Information Extraction, XML technology, etc.

Divide-And-Approximate: A Novel Constraint Push Strategy For Iceberg Cube Mining, Ke Wang, Yuelong Jiang, Jeffrey Xu Yu, Guozhu Dong, Jiawei Han

Kno.e.sis Publications

The iceberg cube mining computes all cells v, corresponding to GROUP BY partitions, that satisfy a given constraint on aggregated behaviors of the tuples in a GROUP BY partition. The number of cells often is so large that the result cannot be realistically searched without pushing the constraint into the search. Previous works have pushed antimonotone and monotone constraints. However, many useful constraints are neither antimonotone nor monotone. We consider a general class of aggregate constraints of the form f(v)θ_σ, where f is an arithmetic function of SQL-like aggregates and θ is one of <, ≤, ≥, > . We propose a …

Cluster Analysis Of Genomic Data With Applications In R, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In this paper, we provide an overview of existing partitioning and hierarchical clustering algorithms in R. We discuss statistical issues and methods in choosing the number of clusters, the choice of clustering algorithm, and the choice of dissimilarity matrix. In particular, we illustrate how the bootstrap can be employed as a statistical method in cluster analysis to establish the reproducibility of the clusters and the overall variability of the followed procedure. We also show how to visualize a clustering result by plotting ordered dissimilarity matrices in R. We present a new R package, hopach, which implements the hybrid clustering method, …

Ranking Complex Relationships On The Semantic Web, Boanerges Aleman-Meza, Christian Halaschek-Wiener, I. Budak Arpinar, Cartic Ramakrishnan, Amit P. Sheth

Kno.e.sis Publications

Industry and academia are both focusing their attention on information retrieval over semantic metadata extracted from the Web, and it is increasingly possible to analyze such metadata to discover interesting relationships. However, just as document ranking is a critical component in today's search engines, the ranking of complex relationships would be an important component in tomorrow's semantic Web engines. This article presents a flexible ranking approach to identify interesting and relevant relationships in the semantic Web. The authors demonstrate the scheme's effectiveness through an empirical evaluation over a real-world data set.

Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection …

A Uniform Approach To Logic Programming Semantics, Pascal Hitzler, Matthias Wendt

Computer Science and Engineering Faculty Publications

Part of the theory of programming and nonymonotonic reasoning concerns the study of fixed-point semantics for these paradigms. Several different semantics have been proposed during the last two decades, and some have been more successful and acknowledged than others. The rationales behind those various semantics have been manifold, depending on one's point of view, which may be that of a programmer or inspired by commonsense reasoning, and consequently the constructions which lead to these semantics are technically very diverse, and the exact relationships between them have not yet been fully understood. In this paper, we present a conceptually new method, …

Level Mapping Characterizations Of Selector-Generated Models For Logic Programs, Sibylle Schwarz, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Assigning semantics to logic programs via selector generated models (Schwarz 2002/2003) extends several semantics, like the stable, the inflationary, and the stable generated semantics, to programs with arbitrary formulae in rule heads and bodies. We study this approach by means of a unifying framework for characterizing different logic programming semantics using level mappings (Hitzler and Wendt 200x, Hitzler 2003), thereby supporting the claim that this framework is very flexible and applicable to very diversely defined semantics.

The Semantic Web In One Day, York Sure, Pascal Hitzler, Andreas Eberhart, Rudi Studer

Computer Science and Engineering Faculty Publications

To gain momentum, technologies for building private semantic Webs or parts of the World Wide semantic Web must become a commodity and easy to integrate. To determine just how far semantic Web technologies have come, we wanted to create a snapshot of what you could do by applying and assembling existing semantic Web technologies - in one day.

Dlp - An Introduction, Denny Vrandecic, Pascal Hitzler, Rudi Studer

Computer Science and Engineering Faculty Publications

DLP - Description Logic Programs - is the name for the common language that is able to integrate knowledge bases described in Description Logic with Logic Programs. In this introduction, we offer a very short overview of DLP, the motivation for it, the benefits it offers and how to use it.

Real-Time Reverse Transcription Pcr For Detection And Quantitative Analysis Of Equine Influenza Virus., Michelle Quinlivan, Eugene Dempsey, Fergus Ryan, Sean Arkins, Ann Cullinnane

Articles

Equine influenza is a cause of epizootic respiratory disease of the equine. The detection of equine influenza virus using real-time Light Cycler reverse transcription (RT)-PCR technology was evaluated over two influenza seasons with the analysis of 171 samples submitted for viral respiratory disease. Increased sensitivity was found in overall viral detection with this system compared to Directigen Flu A and virus isolation, which were 40% and 23%, respectively, that of the RT-PCR. The assay was also evaluated as a viable replacement for the more traditional methods of quantifying equine influenza virus, 50% egg infectious dose and 50% tissue culture infectious …

Validation Of A Multiplex Pcr Assay For The Simultaneous Detection Of Human Papillomavirus And Chlamydia Trachomatis In Cervical Preservcyt Samples., Helen Keegan, Alison Malkin, Mairead Griffin, Fergus Ryan, Helen Lambkin

Articles

No abstract provided.

A Random Rotation Perturbation Approach To Privacy Preserving Data Classification, Keke Chen, Ling Liu

Kno.e.sis Publications

This paper presents a random rotation perturbation approach for privacy preserving data classification. Concretely, we identify the importance of classification-specific information with respect to the loss of information factor, and present a random rotation perturbation framework for privacy preserving data classification. Our approach has two unique characteristics. First, we identify that many classification models utilize the geometric properties of datasets, which can be preserved by geometric rotation. We prove that the three types of classifiers will deliver the same performance over the rotation perturbed dataset as over the original dataset. Second, we propose a multi-column privacy model to address the …

Tontogen: A Synthetic Data Set Generator For Semantic Web Applications, Matthew Perry

Kno.e.sis Publications

No abstract provided.

Variational Bayesian Image Modelling, Li Chen, Feng Jiao, Dale Schuurmans, Shaojun Wang

Kno.e.sis Publications

We present a variational Bayesian framework for performing inference, density estimation and model selection in a special class of graphical models—Hidden Markov Random Fields (HMRFs). HMRFs are particularly well suited to image modelling and in this paper, we apply them to the problem of image segmentation. Unfortunately, HMRFs are notoriously hard to train and use because the exact inference problems they create are intractable. Our main contribution is to introduce an efficient variational approach for performing approximate inference of the Bayesian formulation of HMRFs, which we can then apply to the density estimation and model selection problems that arise when …

Meteor-S Wsdi: A Scalable P2p Infrastructure Of Registries For Semantic Publication And Discovery Of Web Services, Kunal Verma, Kaarthik Sivashanmugam, Amit P. Sheth, Abhijit Patil, Swapna Oundhakar, John Miller

Kno.e.sis Publications

Web services are the new paradigm for distributed computing. They have much to offer towards interoperability of applications and integration of large scale distributed systems. To make Web services accessible to users, service providers use Web service registries to publish them. Current infrastructure of registries requires replication of all Web service publications in all Universal Business Registries. Large growth in number of Web services as well as the growth in the number of registries would make this replication impractical. In addition, the current Web service discovery mechanism is inefficient, as it does not support discovery based on the capabilities of …

From Semantic Search & Integration To Analytics, Amit P. Sheth

Kno.e.sis Publications

Semantics is seen as the key ingredient in the next phase of the Web infrastructure as well as the next generation of enterprise content management. Ontology is the centerpiece of the most prevalent semantic technologies and provides the basis of representing, acquiring, and utilizing knowledge. With the availability of several commercial products and many research tools, specifications and increasing adoption of Semantic Web standards such as RDF for metadata and OWL for ontology representation, ontology-driven techniques and systems have already enabled a new generation of industry strength semantic applications. In particular, Semagix's Freedom has powered applications in leading verticals such …

Discovering Informative Subgraphs In Rdf Graphs, William H. Milnor, Cartic Ramakrishnan, Matthew Perry, Amit P. Sheth, John A. Miller, Krzysztof Kochut

Kno.e.sis Publications

Discovering patterns in graphs has long been an area of interest. In most contemporary approaches to such pattern discovery either quantitative anomalies or frequency of substructure is used to measure the interestingness of a pattern. In this paper we address the issue of discovering informative sub-graphs within RDF graphs. We motivate our work with an example related to Semantic Search. A user might pose a question of the form: ' What are the most relevant ways in which entity X is related to entity Y?' the response to which is a subgraph connecting X to Y. Relevance of the …

Taxaminer: An Experimentation Framework For Automated Taxonomy Bootstrapping, Vipul Kashyap, Cartic Ramakrishnan, Christopher Thomas, Amit P. Sheth

Kno.e.sis Publications

Construction of domain ontologies on the semantic web is a human and resource intensive process, efforts to reduce which are crucial for the Semantic Web to scale. We present a framework for automated taxonomy construction, that involves: (a) generation of a cluster hierarchy from a document corpus using statistical clustering and NLP techniques; (b) extraction of a topic hierarchy from this cluster hierarchy; and (c) assignment of labels to nodes in the topic hierarchy. Metrics for estimating topic hierarchy quality and parameters of an experimentation framework are identified. MEDLINE was the document corpus and MeSH thesaurus was the gold standard.

Framework For Semantic Web Process Composition, Kaarthik Sivashanmugam, John A. Miller, Amit P. Sheth, Kunal Verma

Kno.e.sis Publications

Web services have the potential to revolutionize e-commerce by enabling businesses to interact with each other on the fly. To date, however, Web processes using Web services have been created mostly at the syntactic level. Current composition standards focus on building processes based on the interface description of the participating services. This rigid approach, with its strong coupling between the process and the interface of the participating services, does not allow businesses to dynamically change partners and services. As shown in this article, Web process composition techniques can be enhanced by using semantic process templates to capture the semantic requirements …

Glyde - An Expressive Xml Standard For The Representation Of Glycan, Satya S. Sahoo, Christopher Thomas, Amit P. Sheth, Cory Andrew Henson, William S. York

Kno.e.sis Publications

The amount of glycomics data being generated is rapidly increasing as a result of improvements in analytical and computational methods. Correlation and analysis of this large, distributed data set requires an extensible and flexible representational standard that is also ‘understood’ by a wide range of software applications. An XML-based data representation standard that faithfully captures essential structural details of a glycan moiety along with additional information (such as data provenance) to aid the interpretation and usage of glycan data, will facilitate the exchange of glycomics data across the scientific community. To meet this need, we introduce GLYcan Data Exchange (GLYDE) …

The "Best K" For Entropy-Based Categorical Data Clustering, Keke Chen, Ling Liu

Kno.e.sis Publications

With the growing demand on cluster analysis for categorical data, a handful of categorical clustering algorithms have been developed. Surprisingly, to our knowledge, none has satisfactorily addressed the important problem for categorical clustering – how can we determine the best K number of clusters for a categorical dataset? Since categorical data does not have the inherent distance function as the similarity measure, traditional cluster validation techniques based on the geometry shape and density distribution cannot be applied to answer this question. In this paper, we investigate the entropy property of the categorical data and propose a BkPlot method for determining …