Digital Commons Network^™

Hrests: An Html Microformat For Describing Restful Web Services, Jacek Kopecky, Karthik Gomadam, Tomas Vitvar

Kno.e.sis Publications

The Web 2.0 wave brings, among other aspects, the Programmable Web: increasing numbers of Web sites provide machine-oriented APIs and Web services. However, most APIs are only described with text in HTML documents. The lack of machine-readable API descriptions affects the feasibility of tool support for developers who use these services. We propose a microformat called hRESTS (HTML for RESTful Services) for machine-readable descriptions of Web APIs, backed by a simple service model. The hRESTS microformat describes main aspects of services, such as operations, inputs and outputs. We also present two extensions of hRESTS: SA-REST, which captures the facets of …

Mobile Semantic Computing, Karthik Gomadam, Anupam Joshi, Amit P. Sheth

Kno.e.sis Publications

We propose to organize a special session on research in the intersection of mobile computing, the Semantic Web and Web services.

This session will examine how the research in these areas can serve as a foundation for new architectural and communication paradigms that can enhance service creation, distribution, discovery, integration and utilization in distributed and ubiquitous environments. Some of the initial areas that our early research have highlighted are :

1. Semantic annotation of data in bandwidth constrained environments such as mobile networks to promote efficient bandwidth utilization
2. Possibilities of using microformats such as RDFa and opportunities that can be explored …

Targeted Content Delivery For Social Media Content, Meenakshi Nagarajan, Kamal Baid, Amit P. Sheth, Shaojun Wang

Kno.e.sis Publications

Spotting contextually relevant keywords is fundamental to effective content suggestions on the Web. In this regard, misspellings, entity variations and off-topic discussions in content from Social Media pose unique challenges. Here, we present an algorithm that assists content delivery systems by identifying contextually relevant keywords and eliminating off-topic keywords. A preliminary user study over data from MySpace and Facebook clearly suggests the usefulness of our work in delivering more targeted content suggestions.

Semantic Sensor Web, Amit P. Sheth, Satya S. Sahoo

Kno.e.sis Publications

Sensors are distributed across the globe leading to an avalanche of data about our environment. It is possible today to utilize networks of sensors to detect and identify a multitude of observations, from simple phenomena to complex events and situations. The lack of integration and communication between these networks, however, often isolates important data streams and intensifies the existing problem of too much data and not enough knowledge. With a view to addressing this problem, the semantic sensor Web (SSW) proposes that sensor data be annotated with semantic metadata that will both increase interoperability and provide contextual information essential for …

Services Mashups: The New Generation Of Web Applications, Djamal Benslimane, Schahram Dustdar, Amit P. Sheth

Kno.e.sis Publications

Web services are becoming a major technology for deploying automated interactions between distributed and heterogeneous applications, and for connecting business processes. Service mashups indicate a way to create new Web applications by combining existing Web resources utilizing data and Web APIs. They facilitate the design and development of novel and modern Web applications based on easy-to-accomplish end-user service compositions.

Semantic Sensor Web, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Unsupervised Discovery Of Compound Entities For Relationship Extraction, Cartic Ramakrishnan, Pablo N. Mendes, Shaojun Wang, Amit P. Sheth

Kno.e.sis Publications

In this paper we investigate unsupervised population of a biomedical ontology via information extraction from biomedical literature. Relationships in text seldom connect simple entities. We therefore focus on identifying compound entities rather than mentions of simple entities. We present a method based on rules over grammatical dependency structures for unsupervised segmentation of sentences into compound entities and relationships. We complement the rule-based approach with a statistical component that prunes structures with low information content, thereby reducing false positives in the prediction of compound entities, their constituents and relationships. The extraction is manually evaluated with respect to the UMLS Semantic Network …

Ontology Driven Semantic Provenance For Heterogeneous Bionomics Experimental Data, Satya S. Sahoo, Michael L. Raymer, Cory Andrew Henson, Amit P. Sheth, William S. York

Kno.e.sis Publications

Scientific experimental data generated by all the bionomic technologies is characterized by heterogeneity in its representation formats, constituents, and generation processes and, therefore, also in its usage. Using the proteomics domain we demonstrate the important role of provenance information o manage, interpret and analyze experimental data. We present a novel approach that employs an ontology as a knowledge model to automatically create semantic provenance information for high-throughput mass spectrometry (MS) data in the glycoproteomics domain. The Semantic Provenance Annotation of Data in protEomics (SPADE) implementation is based on the ProPreO ontology, a large-process ontology ( ~500 classes, 40 named relationships …

Strategic Importance Of Higher Education And Research In Positioning Gujarat For Global Competitiveness, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Traveling The Semantic Web Through Space, Theme And Time, Amit P. Sheth, Matthew Perry

Kno.e.sis Publications

In this installment of Semantics and Services, we further develop the idea of spatial, temporal, and thematic (STT) processing of semantic Web data and describe the Web infrastructure needed to support it. Starting from Ramesh Jain's vision of the EventWeb as a view of what's possible with a Web that better accommodates all three dimensions of event-related information (thematic, spatial, and temporal), we outline the architecture needed to support it and current research that aims to realize it.

Approximate Owl-Reasoning With Screech, Tuvshintur Tserendorj, Sebastian Rudolph, Markus Krotzsch, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Applications of expressive ontology reasoning for the Semantic Web require scalable algorithms for deducing implicit knowledge from explicitly given knowledge bases. Besides the development of more effi- cient such algorithms, awareness is rising that approximate reasoning solutions will be helpful and needed for certain application domains. In this paper, we present a comprehensive overview of the Screech approach to approximate reasoning with OWL ontologies, which is based on the KAON2 algorithms, facilitating a compilation of OWL DL TBoxes into Datalog, which is tractable in terms of data complexity. We present three different instantiations of the Screech approach, and report on …

Collaborative Ro1 With Ncbo Semantics And Services Enabled Problem Solving Environment For Trypanosoma Cruzi, Amit P. Sheth, Rick Tarleton, Prashant Doshi, Mark Musen, Natasha Noy, Satya S. Sahoo, Daniel B. Weatherly

Kno.e.sis Publications

No abstract provided.

Monetizing User Activity On Social Networks, Meenakshi Nagarajan, Kamal Baid, Amit P. Sheth, Shaojun Wang

Kno.e.sis Publications

In this work, we investigate techniques to monitize user activity on public forums, marketplaces and groups on social network sites. Our approach involves (a) identifying the monetization potential of user posts and (b) eliminating o- topic content in monetizable posts to use the most relevant keywords for advertising. Our first user study involving 30 users and data from MySpace and Facebook, shows that 52% of ad impressions shown after using our system were more targeted compared to the 30% relevant impressions generated without using our system. A second smaller study suggests that profile ads that are based on user activity …

Joint Extraction Of Compound Entities And Relationships From Biomedical Literature, Cartic Ramakrishnan, Pablo N. Mendes, Rodrigo A.T.S. De Gama, Guilherme C.N. Ferreira, Amit P. Sheth

Kno.e.sis Publications

In this paper we identify some limitations of contemporary information extraction mechanisms in the context of biomedical literature. We present an extraction mechanism that generates structured representations of textual content. Our extraction mechanism achieves this by extracting compound entities, and relationships between them, occuring in text. A detailed evaluation of the relationship and compound entities extracted is presented. Our results show over 62% average precision across 8 relationship types tested with over 82% average precision for compound entity identification1.

Improved Constrained Global Optimization For Estimating Molecular Structure From Atomic Distances, Terri Marie Grant

Mathematics & Statistics Theses & Dissertations

Determination of molecular structure is commonly posed as a nonlinear optimization problem. The objective functions rely on a vast amount of structural data. As a result, the objective functions are most often nonconvex, nonsmooth, and possess many local minima. Furthermore, introduction of additional structural data into the objective function creates barriers in finding the global minimum, causes additional computational issues associated with evaluating the function, and makes physical constraint enforcement intractable. To combat the computational problems associated with standard nonlinear optimization formulations, Williams et al. (2001) proposed an atom-based optimization, referred to as GNOMAD, which complements a simple interatomic distance …

Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan

Computer Science Theses & Dissertations

Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. …

Mutual Information Without The Influence Of Phylogeny Or Entropy Dramatically Improves Residue Contact Prediction, Stanley Dunn, Lindi Wahl, Gregory Gloor

Stanley D Dunn

Motivation: Compensating alterations during the evolution of protein families give rise to coevolving positions that contain important structural and functional information. However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions.

Results: We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Removal of this background results in a metric, MIp, that correctly identifies substantially more coevolving positions in protein families than any existing method. A significant fraction of these …

Tetra-N-Butyl­Ammonium Bis­(2,2-Dicyano­Ethyl­Ene-1,1-Dithiol­Ato)Palladium(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen

Daron E Janzen, Ph.D.

No abstract provided.

Tetra-N-Butyl-Ammonium Bis-(1,1-Dicyano-Ethyl-Ene-2,2-Dithiol-Ato)Platinum(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen

Daron E Janzen, Ph.D.

No abstract provided.

Pisciforma, Setisura, And Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based On 18s Rdna Sequences: A Reply To Sun Et Al. (2006), T. Heath Ogden

T. Heath Ogden

No abstract provided.

Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden

T. Heath Ogden

We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher-level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non-monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta …