Life Sciences Commons^™

Reproducible Research: A Bioinformatics Case Study, Robert Gentleman

Bioconductor Project Working Papers

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2004), suggests a methodology and basic infrastructure that can be used to publish documents in …

Classification Using Generalized Partial Least Squares, Beiying Ding, Robert Gentleman

Bioconductor Project Working Papers

The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in which to study various aspects of gene functions but they also present challenge of analyzing data with large number of covariates and few samples. As an integral part of machine learning, classification of samples into two or more categories is almost always of interest to scientists. In this paper, we address the question of classification in this setting by extending partial least squares (PLS), a popular dimension reduction tool in chemometrics, in …

Meteor-S Web Service Annotation Framework, Abhijit A. Patil, Swapna A. Oundhakar, Amit P. Sheth, Kunal Verma

Kno.e.sis Publications

The World Wide Web is emerging not only as an infrastructure for data, but also for a broader variety of resources that are increasingly being made available as Web services. Relevant current standards like UDDI, WSDL, and SOAP are in their fledgling years and form the basis of making Web services a workable and broadly adopted technology. However, realizing the fuller scope of the promise of Web services and associated service oriented architecture will requite further technological advances in the areas of service interoperation, service discovery, service composition, and process orchestration. Semantics, especially as supported by the use of ontologies, …

Sempl: A Semantic Portal, Matthew Perry, Eric Stiles

Kno.e.sis Publications

Semantic Web technology is intended for the retrieval, collection, and analysis of meaningful data with significant automation afforded by machine understandability of data [1]. As one illustration of semantic web technology in action, we present SEMPL, a semantic web portal for the Large Scale Distributed Information Systems lab (LSDIS) at the University of Georgia. SEMPL, which is powered by a state of the art commercial system, Semagix Freedom [7], uses an ontology-driven approach to provide semantic browsing, linking, and contextual querying of content within the portal. By using the ontology based information integration technique, SEMPL can specify the context of …

Indexing Genomic Databases, Gina Cooper, Michael L. Raymer, Travis E. Doom, Dan E. Krane, Natsuhiko Futamura

Kno.e.sis Publications

Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata …

Quality Of Service For Workflows And Web Service Processes, Jorge Cardoso, Amit P. Sheth, John A. Miller, Jonathan Arnold, Krzysztof J. Kochut

Kno.e.sis Publications

Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows or Web processes for e-commerce and Web service applications, suppliers and customers define a binding agreement or contract between the two parties, specifying quality of service (QoS) items such as products or services to be delivered, deadlines, quality of products, and cost of services. The management of QoS metrics directly impacts the success of organizations participating in e-commerce. Therefore, when services or products are created or managed using workflows or Web processes, the underlying workflow engine must accept …

Prediction Of Rna-Binding Proteins From Primary Sequence By A Support Vector Machine Approach., Lian Yi Han, Cong Zhong Cai, Siaw Ling Lo, Maxey Chung, Yu Zong Chen

Research Collection School Of Computing and Information Systems

Elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. Computational methods have been developed for the prediction of protein-protein interactions. But insufficient attention has been paid to the prediction of protein-RNA interactions, which play central roles in regulating gene expression and certain RNA-mediated enzymatic processes. This work explored the use of a machine learning method, support vector machines (SVM), for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to recognize RNA-binding proteins. A total …

Mixture Models For Assessing Differential Expression In Complex Tissues Using Microarray Data, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

The use of DNA microarrays has become quite popular in many scientific and medical disciplines, such as in cancer research. One common goal of these studies is to determine which genes are differentially expressed between cancer and healthy tissue, or more generally, between two experimental conditions. A major complication in the molecular profiling of tumors using gene expression data is that the data represent a combination of tumor and normal cells. Much of the methodology developed for assessing differential expression with microarray data has assumed that tissue samples are homogeneous. In this article, we outline a general framework for determining …

Bioconductor: Open Software Development For Computational Biology And Bioinformatics, Robert C. Gentleman, Vincent J. Carey, Douglas J. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Guenther Sawitzki, Colin Smith, Gordon K. Smyth, Luke Tierney, Yee Hwa Yang, Jianhua Zhang

Bioconductor Project Working Papers

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have …

Early Work In Database Research On Schema Mapping/Merging/Transformation, Semantic Heterogeneity, And Use Of Ontology And Description Logics For Schematic And Semantic Integration, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Exploiting Syntactic, Semantic And Lexical Regularities In Language Modeling Via Directed Markov Random Fields, Shaojun Wang, Shaomin Wang, Russell Greiner, Dale Schuurmans, Li Cheng

Kno.e.sis Publications

No abstract provided.

On The Decidability Of The Termination Problem Of Active Database Systems, James Bailey, Guozhu Dong, K. Rammamohanarao

Kno.e.sis Publications

Active database systems enhance the functionality of traditional databases through the use of active rules or ‘triggers’. One of the principal analysis questions for such systems is that of termination—is it possible for the rules to recursively activate one another indefinitely, given an initial triggering event. In this paper, we study the decidability of the termination problem, our aim being to delimit the boundary between the decidable and the undecidable. We present results for two broad types of variations, variations in rule syntax and variations in meta level features. Within each of these, we identify members close to the …

Evaluation Of Multiple Models To Distinguish Closely Related Forms Of Disease Using Dna Microarray Data: An Application To Multiple Myeloma, Johanna S. Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J. Crowley

Pomona Faculty Publications and Research

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is …

Semantic Integration Of Glycomics Data And Information, William S. York, Amit P. Sheth, Krzysztof J. Kochut, John A. Miller, Christopher Thomas, Karthik Gomadam, X. Yi, Meenakshi Nagarajan

Kno.e.sis Publications

No abstract provided.

Discovering And Ranking Semantic Associations Over A Large Rdf Metabase, Christian Halaschek-Wiener, Boanerges Aleman-Meza, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Information retrieval over semantic metadata has recently received a great amount of interest in both industry and academia. In particular, discovering complex and meaningful relationships among this data is becoming an active research topic. Just as ranking of documents is a critical component of today's search engines, the ranking of relationships will be essential in tomorrow's semantic analytics engines. Building upon our recent work on specifying these semantic relationships, which we refer to as Semantic Associations, we demonstrate a system where these associations are discovered among a large semantic metabase represented in RDF. Additionally we employ ranking techniques to provide …

Service Oriented Architectures And Semantic Web Processes, Francisco Cubera, Kunal Verma, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Semantic Visualization: Interfaces For Exploring And Exploiting Ontology, Knowledgebase, Heterogeneous Content And Complex Relationships, Amit P. Sheth, David Avant

Kno.e.sis Publications

Technology platforms and products for ontology-driven process of semantic applications that serve both Enterprise wide and pan-Web needs are both available and being deployed. Similar to the development of enterprise software applications, the creation of an ontology driven semantic application can be described as a set of distinct phases that compose a lifecycle. From conception to deployment, these phases involve human interaction with a broad variety of information, identified as heterogeneous data, metadata, knowledge and ontology. Based on experience spanning academic research at the LSDIS lab through deployed commercial semantic applications based on Semagix Freedom, this paper provides examples of …

Semantic Web Research Center Report: Lsdis Lab, Research In Semantic Bioinformatics, Semantic Analytics And Semantic Web Processes, Amit P. Sheth

Kno.e.sis Publications

The LSDIS Lab advances the field of distributed information systems by researching semantic techniques for exploiting heterogeneous multimedia information and improving processes, encompassing the central promise of the Semantic Web initiative. It is pursuing cutting edge research in ontology development for demanding scientific domains, semantic heterogeneity and integration, complex relationships discovery and semantic analytics, and Semantic Web services and processes. Past work of the LSDIS lab can be characterized by keywords: semantic interoperability, syntactic and semantic metadata for text and digital media, metadata based integration of Web content, ontology-driven information systems, multi-ontology query processing, transactional workflows and workflow management. Significant …

Evaluating The Disparity Of Female Breast Cancer Mortality Among Racial Groups - A Spatiotemporal Analysis, Chiehwen E. Hsu, Holly Jacobson, Francisco Soto Mas

Faculty, Staff and Student Publications

Background The literature suggests that the distribution of female breast cancer mortality demonstrates spatial concentration. There remains a lack of studies on how the mortality burden may impact racial groups across space and over time. The present study evaluated the geographic variations in breast cancer mortality in Texas females according to three predominant racial groups (non-Hispanic White, Black, and Hispanic females) over a twelve-year period. It sought to clarify whether the spatiotemporal trend might place an uneven burden on particular racial groups, and whether the excess trend has persisted into the current decade.

Methods The Spatial Scan Statistic was employed …

Detecting Spatiotemporal Clusters Of Accidental Poisoning Mortality Among Texas Counties, Us, 1980 – 2001, Ella T. Nkhoma, Chiehwen E. Hsu, Victoria I. Hunt, Ann M. Harris

Faculty, Staff and Student Publications

Background Accidental poisoning is one of the leading causes of injury in the United States, second only to motor vehicle accidents. According to the Centers for Disease Control and Prevention, the rates of accidental poisoning mortality have been increasing in the past fourteen years nationally. In Texas, mortality rates from accidental poisoning have mirrored national trends, increasing linearly from 1981 to 2001. The purpose of this study was to determine if there are spatiotemporal clusters of accidental poisoning mortality among Texas counties, and if so, whether there are variations in clustering and risk according to gender and race/ethnicity. The Spatial …

Semantic (Web) Technology In Action: Ontology Driven Information Systems For Search, Integration, And Analysis, Amit P. Sheth, Cartic Ramakrishnan

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 information systems applications. In this context, we review some of the reservations expressed about the viability of the Semantic Web. We respond to these by identifying a Semantic Technology that supports the key capabilities also needed to realize the Semantic Web vision, namely representing, acquiring and utilizing knowledge. Given that scalability is a key challenge, we briefly review our observations from developing three classes of real world applications and corresponding technology components: search/browsing, integration, and analytics. We distinguish …

Semantic Web Processes: Semantics Enabled Annotation, Discovery, Composition, And Orchestration Of Web Scale Processes, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

This tutorial deals with the evolution of inter- Enterprise and Web scale process to support e-commerce and e-services. It taps into the promises of two of the hottest R&D and technology areas: Web services and the Semantic Web. It presents how applying semantics to each of the steps in the Semantic Web Process lifecycle can help address critical issues in reuse, integration and scalability.

Validating And Refining Clusters Via Visual Rendering, Keke Chen, Ling Liu

Kno.e.sis Publications

The automatic clustering algorithms are known to work well in dealing with clusters of regular shapes, e.g. compact spherical/elongated shapes, but may incur higher error rates when dealing with arbitrarily shaped clusters. Although some efforts have been devoted to addressing the problem of skewed datasets, the problem of handling clusters with irregular shapes is still in its infancy, especially in terms of dimensionality of the datasets and the precision of the clustering results considered. Not surprisingly, the statistical indices works ineffective in validating clusters of irregular shapes, too. We address the problem of clustering and validating arbitrarily shaped clusters with …

Semantic E-Workflow Composition, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

Systems and infrastructures are currently being developed to support Web services. The main idea is to encapsulate an organization's functionality within an appropriate interface and advertise it as Web services. While in some cases Web services may be utilized in an isolated form, it is normal to expect Web services to be integrated as part of workflow processes. The composition of workflow processes that model e-service applications differs from the design of traditional workflows, in terms of the number of tasks (Web services) available to the composition process, in their heterogeneity, and in their autonomy. Therefore, two problems need to …

Towards (Semi-) Automatic Generation Of Bio-Medical Ontologies, Vipul Kashyap, Cartic Ramakrishnan, Thomas Rindflesch

Kno.e.sis Publications

The design and construction of domain specific ontologies and taxonomies requires allocation of huge resources in terms of cost and time. These efforts are human intensive and we need to explore ways of minimizing human involvement and other resources. In the biomedical domain, we seek to leverage resources such as the UMLS1 Metathesaurus and NLP-based applications such as MetaMap2 in conjunction with statistical clustering techniques, to (partially) automate the process. This is expected to be useful to the team involved in developing MeSH and other biomedical taxonomies to identify gaps in the existing taxonomies, and to be able to quickly …

What Can Semantics Do For Bioinformatics?, Amit P. Sheth

Kno.e.sis Publications

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Semantic Web In Action: Ontology-Driven Information Search, Integration And Analysis, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Christian Halaschek-Wiener, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Discovering complex and meaningful relationships, which we call Semantic Associations, is an important challenge. Just as ranking of documents is a critical component of today's search engines, ranking of relationships will be essential in tomorrow's semantic search engines that would support discovery and mining of the Semantic Web. Building upon our recent work on specifying types of Semantic Associations in RDF graphs, which are possible to create through semantic metadata extraction and annotation, we discuss a framework where ranking techniques can be used to identify more interesting and more relevant Semantic Associations. Our techniques utilize alternative ways of specifying the …

Continuity Of Semantic Operators In Logic Programming And Their Approximation By Artificial Neural Networks, Pascal Hitzler, Anthony K. Seda

Computer Science and Engineering Faculty Publications

One approach to integrating first-order logic programming and neural network systems employs the approximation of semantic operators by feedforward networks. For this purpose, it is necessary to view these semantic operators as continuous functions on the reals. This can be accomplished by endowing the space of all interpretations of a logic program with topologies obtained from suitable embeddings. We will present such topologies which arise naturally out of the theory of logic programming, discuss continuity issues of several well-known semantic operators, and derive some results concerning the approximation of these operators by feedforward neural networks.

Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Chris Halaschek, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Discovering complex and meaningful relationships, which we call Semantic Associations, is an important challenge. Just as ranking of documents is a critical component of today's search engines, ranking of relationships will be essential in tomorrow's semantic search engines that would support discovery and mining of the Semantic Web. Building upon our recent work on specifying types of Semantic Associations in RDF graphs, which are possible to create through semantic metadata extraction and annotation, we discuss a framework where ranking techniques can be used to identify more interesting and more relevant Semantic Associations. Our techniques utilize alternative ways of specifying the …