Life Sciences Commons^™

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Computer and Electronics Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Overview Of Contrast Data Mining As A Field And Preview Of An Upcoming Book, Guozhu Dong, James Bailey

Kno.e.sis Publications

This report provides an overview of the field of contrast data mining and its applications, and offers a preview of an upcoming book on the topic. The importance of contrasting is discussed and a brief survey is given covering the following topics: general definitions and terminology for contrast patterns, representative contrast pattern mining algorithms, applications of contrast mining for fundamental data mining tasks such as classification and clustering, applications of contrast mining in bioinformatics, medicine, blog analysis, image analysis and subgroup mining, results on contrast based dataset similarity measure, and on analyzing item interaction in contrast patterns, and open research …

Computing Inconsistency Measure Based On Paraconsistent Semantics, Pascal Hitzler, Yue Ma, Guilin Qi

Computer Science and Engineering Faculty Publications

Measuring inconsistency in knowledge bases has been recognized as an important problem in several research areas. Many methods have been proposed to solve this problem and a main class of them is based on some kind of paraconsistent semantics. However, existing methods suffer from two limitations: (i) they are mostly restricted to propositional knowledge bases; (ii) very few of them discuss computational aspects of computing inconsistency measures. In this article, we try to solve these two limitations by exploring algorithms for computing an inconsistency measure of first-order knowledge bases. After introducing a four-valued semantics for first-order logic, we define an …

The Knowledge-Driven Exploration Of Integrated Biomedical Knowledge Sources Facilitates The Generation Of New Hypotheses, Vinh Nguyen, Olivier Bodenreider, Todd Minning, Amit P. Sheth

Kno.e.sis Publications

Knowledge gained from the scientific literature can complement newly obtained experimental data in helping researchers understand the pathological processes underlying diseases. However, unless the scientific literature and experimental data are semantically integrated, it is generally difficult for scientists to exploit the two sources effectively. We argue that, in addition to the semantic integration of heterogeneous knowledge sources, the usability of the integrated resource by scientists is dependent upon the availability of knowledge visualization and exploration tools. Moreover, the integration techniques must be scalable and the exploration interfaces must be easy to use by bench scientists. The end goal of such …

Demonstration: Real-Time Semantic Analysis Of Sensor Streams, Harshal Patni, Cory Andrew Henson, Michael Cooney, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The emergence of dynamic information sources – including sensor networks – has led to large streams of real-time data on the Web. Research studies suggest, these dynamic networks have created more data in the last three years than in the entire history of civilization, and this trend will only increase in the coming years [1]. With this coming data explosion, real-time analytics software must either adapt or die [2]. This paper focuses on the task of integrating and analyzing multiple heterogeneous streams of sensor data with the goal of creating meaningful abstractions, or features. These features are then temporally aggregated …

Demonstration: Secure - Semantics Empowered Rescue Environment, Pratikkumar Desai, Cory Andrew Henson, Pramod Anantharam, Amit P. Sheth

Kno.e.sis Publications

This paper demonstrates a Semantic Web enabled system for collecting and processing sensor data within a rescue environment. The real-time system collects heterogeneous raw sensor data from rescue robots through a wireless sensor network. The raw sensor data is converted to RDF using the Semantic Sensor Network (SSN) ontology and further processed to generate abstractions used for event detection in emergency scenarios.

Sempush: Privacy-Aware And Scalable Broadcasting For Semantic Microblogging, Pavan Kapanipathi, Julia Anaya, Alexandre Passant

Kno.e.sis Publications

Users of traditional microblogging platforms such as Twitter face drawbacks in terms of (1) Privacy of status updates as a followee - reaching undesired people (2) Information overload as a follower - receiving uninteresting microposts from followees. In this paper we demonstrate distributed and user-controlled dissemination of microposts using SMOB (semantic microblogging framework) and Semantic Hub (privacy-aware implementation of PuSH3 protocol) . The approach leverages users' Social Graph to dynamically create group of followers who are eligible to receive micropost. The restrictions to create the groups are provided by the followee based on the hastags in the micropost. Both SMOB …

A Domain Specific Language For Enterprise Grade Cloud-Mobile Hybrid Applications, Ajith H. Ranabahu, E. Michael Maximilien, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

Cloud computing has changed the technology landscape by offering flexible and economical computing resources to the masses. However, vendor lock-in makes the migration of applications and data across clouds an expensive proposition. The lock-in is especially serious when considering the new technology trend of combining cloud with mobile devices.

In this paper, we present a domain specific language (DSL) that is purposely created for generating hybrid applications spanning across mobile devices as well as computing clouds. We propose a model-driven development process that makes use of a DSL to provide sufficient programming abstractions over both cloud and mobile features. We …

Semantic Annotation And Search For Resources In The Next Generation Web With Sa-Rest, Ajith H. Ranabahu, Amit P. Sheth, Maryam Panahiazar, Sanjaya Wijeratne

Kno.e.sis Publications

SA-REST, the W3C member submission, can be used for supporting a wide variety of Plain Old Semantic HTML (POSH) annotation capabilities on any type of Web resource. Kino framework and tools provide support of capabilities to realize SA-RESTs promised value. These tools include (a) a browser-plugin to support annotation of a Web resource (including services) with respect to an ontology, domain model or vocabulary, (b) an annotation aware indexing engine and (c) faceted search and selection of the Web resources. At one end of the spectrum, we present Kino^E (aka Kino for Enterprise) which uses NCBO formal ontologies and …

Personalized Filtering Of The Twitter Stream, Pavan Kapanipathi, Fabrizio Orlandi, Amit P. Sheth, Alexandre Passant

Kno.e.sis Publications

With the rapid growth in users on social networks, there is a corresponding increase in user-generated content, in turn resulting in information overload. On Twitter, for example, users tend to receive uninterested information due to their non-overlapping interests from the people whom they follow. In this paper we present a Semantic Web approach to filter public tweets matching interests from personalized user profiles. Our approach includes automatic generation of multi-domain and personalized user profiles, filtering Twitter stream based on the generated profiles and delivering them in real-time. Given that users interests and personalization needs change with time, we also discuss …

Semantic Computing In Real-World: Vertical And Horizontal Application Within Enterprise And On The Web, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Structural Analysis Of The Hot Spots In The Binding Between H1n1 Ha And The 2di Antibody: Do Mutations Of H1n1 From 1918 To 2009 Affect Much On This Binding?, Qian Liu, Steven C. H. Hoi, Chinh T. T. Su, Zhenhua Li, Chee-Keong Kwoh, Limsoon Wong, Jinyan Li

Research Collection School Of Computing and Information Systems

Worldwide and substantial mortality caused by the 2009 H1N1 influenza A has stimulated a new surge of research on H1N1 viruses. An epitope conservation has been learned in the HA1 protein that allows antibodies to cross-neutralize both 1918 and 2009 H1N1. However, few works have thoroughly studied the binding hot spots in those two antigen–antibody interfaces which are responsible for the antibody cross-neutralization. We apply predictive methods to identify binding hot spots at the epitope sites of the HA1 proteins and at the paratope sites of the 2D1 antibody. We find that the six mutations at the HA1's epitope from …

Kino: A Generic Document Management System For Biologists Using Sa-Rest And Faceted Search, Ajith Harshana Ranabahu, Priti Parikh, Maryam Panahiazar, Amit P. Sheth

Kno.e.sis Publications

Document management has become an important consideration for the scientific community over the last decade. Human knowledge is central to many scientific domains, thus it is not possible to completely automate the document management process. Managing scientific documents require a semi-automatic approach to overcome issues of large volume, yet support the human participation in the process. In this paper we present Kino, a set of tools that streamline the document management process in life science domains. Kino is integrated with National Center for Biomedical Ontology (NCBO), providing scientists access to quality domain models. Annotated documents are indexed using a faceted …

Citizen Sensing: Opportunities And Challenges In Mining Social Signals And Perceptions, Amit P. Sheth

Kno.e.sis Publications

Millions of persons have become 'citizens' of an Internet- or Web-enabled social community. Web 2.0 fostered the open environment and applications for tagging, blogging, wikis, and social networking sites that have made information consumption, production, and sharing so incredibly easy. An interconnected network of people who actively observe, report, collect, analyze, and disseminate information via text, audio, or video messages, increasingly through pervasively connected mobile devices, has led to what we term citizen sensing. In this talk, we review recent progress in supporting collective intelligence through intelligent processing of citizen sensing. Key issues we cover in this talk are: - …

Local Closed World Semantics: Keep It Simple, Stupid!, Adila Krishnadhi, Kunal Sengupta, Pascal Hitzler

Computer Science and Engineering Faculty Publications

A combination of open and closed-world reasoning (usually called local closed world reasoning) is a desirable capability of knowledge representation formalisms for Semantic Web applications. However, none of the proposals made to date for extending description logics with local closed world capabilities has had any significant impact on applications. We believe that one of the key reasons for this is that current proposals fail to provide approaches which are intuitively accessible for application developers at the same time are applicable, as extensions, to expressive description logics as SROIQ, which underlies the Web Ontology Language OWL.

In this paper, we propose …

Web Wisdom: An Essay On How Web 2.0 And Semantic Web Can Foster A Global Knowledge Society, Christopher Thomas, Amit P. Sheth

Kno.e.sis Publications

Admittedly this is a presumptuous title that should never be used when reporting on individual research advances. Wisdom is just not a scientific concept. In this case, though, we are reporting on recent developments on the web that lead us to believe that the web is on the way to providing a platform for not only information acquisition and business transactions but also for large scale knowledge development and decision support. It is likely that by now every web user has participated in some sort of social function or knowledge accumulating function on the web, many times without even being …

A Study On Facility Planning Using Discrete Event Simulation: Case Study Of A Grain Delivery Terminal., Sarah M. Asio

Department of Industrial and Management Systems Engineering: Dissertations, Theses, and Student Research

The application of traditional approaches to the design of efficient facilities can be tedious and time consuming when uncertainty and a number of constraints exist. Queuing models and mathematical programming techniques are not able to capture the complex interaction between resources, the environment and space constraints for dynamic stochastic processes. In the following study discrete event simulation is applied to the facility planning process for a grain delivery terminal. The discrete event simulation approach has been applied to studies such as capacity planning and facility layout for a gasoline station and evaluating the resource requirements for a manufacturing facility. To …

Efficient Unfolding Pattern Recognition In Single Molecule Force Spectroscopy Data, Bill Andreopoulos, Dirk Labudde

Faculty Publications, Computer Science

BackgroundSingle-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived.ResultsIn the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise …

Smob: The Best Of Both Worlds, Alexandre Passant, Julia Anaya, Owen Sacco, Pavan Kapanipathi

Kno.e.sis Publications

This paper presents the architecture of SMOB and the way it combines Semantic Web standards (RDF(S) / SPARQL) and new protocols such as PubSubHubbub to enable a Federated and Privacy-Aware Social Web.

Local Closed-World Reasoning With Description Logics Under The Well-Founded Semantics, Matthias Knorr, Jose Julio Alferes, Pascal Hitzler

Computer Science and Engineering Faculty Publications

An important question for the upcoming Semantic Web is how to best combine open world ontology languages, such as the OWL-based ones, with closed world rule-based languages. One of the most mature proposals for this combination is known as hybrid MKNF knowledge bases (Motik and Rosati, 2010 [52]), and it is based on an adaptation of the Stable Model Semantics to knowledge bases consisting of ontology axioms and rules. In this paper we propose a well-founded semantics for nondisjunctive hybrid MKNF knowledge bases that promises to provide better efficiency of reasoning, and that is compatible with both the OWL-based …

Automatic Domain Model Creation Using Pattern-Based Fact Extraction, Christopher Thomas, Pankaj Mehra, Wenbo Wang, Amit P. Sheth, Gerhard Weikum, Victor Chan

Kno.e.sis Publications

This paper describes a minimally guided approach to automatic domain model creation. The first step is to carve an area of interest out of the Wikipedia hierarchy based on a simple query or other starting point. The second step is to connect the concepts in this domain hierarchy with named relationships. A starting point is provided by Linked Open Data, such as DBPedia. Based on these community-generated facts we train a pattern-based fact-extraction algorithm to augment a domain hierarchy with previously unknown relationship occurrences. Pattern vectors are learned that represent occurrences of relationships between concepts. The process described can be …

Privacy-By-Design In Federated Social Web Applications, Alexandre Passant, Owen Sacco, Julia Anaya, Pavan Kapanipathi

Kno.e.sis Publications

No abstract provided.

What's Happening In Semantic Web ... And What Fca Could Have To Do With It, Pascal Hitzler

Computer Science and Engineering Faculty Publications

The Semantic Web is gaining momentum. Driven by over 10 years of focused project funding in the US and the EU, Semantic Web Technologies are now entering application areas in industry, academia, government, and the open Web.

The Semantic Web is based on the idea of describing the meaning - or semantics - of data on the Web using metadata - data that describes other data - in the form of ontologies, which are represented using logic-based knowledge representation languages. Central to the transfer of Semantic Web into practice is the Linked Open Data effort, which has already resulted in …

Trust Networks: Interpersonal, Social, And Sensor, Krishnaprasad Thirunarayan, Pramod Anantharam

Kno.e.sis Publications

Trust relationships occur naturally in many diverse contexts such as ecommerce, interpersonal interactions, social networks, sensor web, etc. As agents providing content and services become increasingly removed from the agents that consume them, the issue of robust trust inference and update become critical. Unfortunately, there is neither a universal notion of trust that is applicable to all domains nor a clear explication of its semantics or computation in many situations. In this beginner's level tutorial, we motivate the trust problem, explain the relevant concepts, summarize research in modeling trust and gleaning trustworthiness, and discuss challenges confronting us in this process.

Beespace Navigator: Exploratory Analysis Of Gene Function Using Semantic Indexing Of Biological Literature, Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz

Research Collection School Of Computing and Information Systems

With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments …

Protein Structure – Based Method For Identification Of Horizontal Gene Transfer In Bacteria, Swetha Billa

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Horizontal Gene Transfer is defined as the movement of genetic material from one strain of species to another. Bacteria, being an asexual organism were always believed to transfer genes vertically. But recent studies provide evidence that shows bacteria can also transfer genes horizontally.

HGT plays a major role in evolution and medicine. It is the major contributor in bacterial evolution, enabling species to acquire genes to adapt to the new environments. Bacteria are also believed to develop drug resistance to antibiotics through the phenomenon of HGT. Therefore further study of HGT and its implications is necessary to understand the effects …

Dicarbonyldichloridobis(Trimethylphosphane)Iron(Ii)–Carbonyldichloridotris(Trimethylphosphane)Iron(Ii)–Tetrahydrofuran (1/1/2), Nigam Rath, Meghan Stouffer, Matthew Janssen, John Bleeke

Chemistry & Biochemistry Faculty Works

The asymmetric unit of the title crystal, [FeCl2(C3H9P)3(CO)]·[FeCl2(C3H9P)2(CO)2]·2C4H8O, contains half mol­ecules of the two closely related FeII complexes lying on mirror planes and a tetra­hydro­furan solvent mol­ecule, one C atom of which is disordered over two sets of sites with site occupancy factors 0.633 (9) and 0.367 (9). In both FeII complex mol­ecules, a distorted octa­hedral coordination geometry has been observed around the Fe atoms. Weak intermolecular C-H...O inter­actions are observed in the crystal structure.

Computational Complexity Of Approximate And Precise Data With Constraint Automaton, Dipty Singh

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The DNA molecules packaged in structures called chromosomes within the cells of living organisms encode hereditary information that is passed on to their offspring. Using transcription and translation, the genes within these DNA molecules help in protein synthesis. Thus chromosomal DNA serves as a blueprint for the chemical processes of life.

In order to analyze a DNA sequence by currently available technology, we have to cut it into small fragments, e.g. by using restriction enzymes. The application of different restriction enzymes to the multiple copies of the same DNA sequence generates many overlapping fragments. In order to construct the original …

Identifying And Implementing The Underlying Operators For Nuclear Magnetic Resonance Based Metabolomics Data Analysis, Ashwin Manjunatha, Ajith H. Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The science of metabolomics is a relatively young field that requires intensive signal processing and multivariate data analysis for interpretation of experimental results. The lack of integration and standardization for metabolomics compounded by the complexity of the experimental data has lead to a fragmented research community. While efforts have been undertaken to approach these problems, the efforts to develop a set of standards for reporting processing and analysis procedures has stalled.

In this paper, we propose a set of fundamental operators for nuclear magnetic resonance(NMR) based metabolomics. These operators are implementation independent, and can be used to easily and precisely …

Scireader Enables Reading Of Medical Content With Instantaneous Definitions, Patrick R. Gradie, Megan Litster, Rinu Thomas, Jay Vyas, Martin Schiller

Life Sciences Faculty Research

Background

A major problem patients encounter when reading about health related issues is document interpretation, which limits reading comprehension and therefore negatively impacts health care. Currently, searching for medical definitions from an external source is time consuming, distracting, and negatively impacts reading comprehension and memory of the material.

Methods

SciReader was built as a Java application with a Flex-based front-end client. The dictionary used bySciReader was built by consolidating data from several sources and generating new definitions with a standardized syntax. The application was evaluated by measuring the percentage of words defined in different documents. A survey was used …