Databases and Information Systems Commons^™

The Economics Of The Right To Be Forgotten, Byung-Cheol Kim, Jin Yeub Kim

Department of Economics: Faculty Publications

Scholars and practitioners debate whether to expand the scope of the right to be forgotten—the right to have certain links removed from search results—to encompass global search results. The debate centers on the assumption that the expansion will increase the incidence of link removal, which reinforces privacy while hampering free speech. We develop a game-theoretic model to show that the expansion of the right to be forgotten can reduce the incidence of link removal. We also show that the expansion does not necessarily enhance the welfare of individuals who request removal and that it can either improve or reduce societal …

So What Are You Going To Do With That? The Promises And Pitfalls Of Massive Data Sets, Sigrid Anderson Cordell, Melissa Gomis

University of Nebraska-Lincoln Libraries: Faculty Publications

This article takes as its case study the challenge of data sets for text mining, sources that offer tremendous promise for digital humanities (DH) methodology but present specific challenges for humanities scholars. These text sets raise a range of issues: What skills do you train humanists to have? What is the library’s role in enabling and supporting use of those materials? How do you allocate staff? Who oversees sustainability and data management? By addressing these questions through a specific use case scenario, this article shows how these questions are central to mapping out future directions for a range of library …

Towards Building A Review Recommendation System That Trains Novices By Leveraging The Actions Of Experts, Shilpa Khanal

School of Computing: Dissertations, Theses, and Student Research

Online reviews increase consumer visits, increase the time spent on the website, and create a sense of community among the frequent shoppers. Because of the importance of online reviews, online retailers such as Amazon.com and eOpinions provide detailed guidelines for writing reviews. However, though these guidelines provide instructions on how to write reviews, reviewers are not provided instructions for writing product-specific reviews. As a result, poorly-written reviews are abound and a customer may need to scroll through a large number of reviews, which could be up to 6000 pixels down from the top of the page, in order to find …

Past Meets Future: Combining Gis, 3d Technologies, And Legacy Data To Reanalyze Ceramics At Copan, Honduras, Stephanie Sterling, Heather Richards-Rissetto, René Viel

UCARE: Research Products

The archaeological site of Copán—a UNESCO World Heritage Site in Honduras—was a primary center for cultural and economic exchange in the Maya world from the fifth to ninth centuries. Our research investigates the sociopolitical climate of the city immediately preceding this collapse. This poster presents the results of a pilot study intended to evaluate the potential of using a combination of digital technologies and legacy data to reanalyze a subset of diagnostic ceramics from select sites outside of Copan’s urban core. Our methods involved:

(1) Applying photogrammetry to generate 3D models for approximately 30 potentially temporally-diagnostic ceramic types

(2) Digitizing, …

Bioinformatics Approaches To Single-Cell Analysis In Developmental Biology, Dicle Yalcin, Zeynep M. Hakguder, Hasan H. Otu

Department of Electrical and Computer Engineering: Faculty Publications

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging …

Dietary Microrna Database (Dmd): An Archive Database And Analytic Tool For Food-Borne Micrornas, Kevin Chiang, Jiang Shu, Janos Zempleni, Juan Cui

School of Computing: Faculty Publications

With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental …

Ultimate Codes: Near-Optimal Mds Array Codes For Raid-6, Zhijie Huang, Hong Jiang, Chong Wang, Ke Zhou, Yuhong Zhao

School of Computing: Technical Reports

As modern storage systems have grown in size and complexity, RAID-6 is poised to replace RAID-5 as the dominant form of RAID architectures due to its ability to protect against double disk failures. Many excellent erasure codes specially designed for RAID-6 have emerged in recent years. However, all of them have limitations. In this paper, we present a class of near perfect erasure codes for RAID-6, called the Ultimate codes. These codes encode, update and decode either optimally or nearly optimally, regardless of what the code length is. This implies that utilizing these codes we can build highly efficient and …

Cms Use Of A Data Federation, Kenneth A. Bloom, C.

Kenneth Bloom Publications

CMS is in the process of deploying an Xrootd based infrastructure to facilitate a global data federation. The services of the federation are available to export data from half the physical capacity and the majority of sites are configured to read data over the federation as a back-up. CMS began with a relatively modest set of use-cases for recovery of failed local file opens, debugging and visualization. CMS is finding that the data federation can be used to support small scale analysis and load balancing. Looking forward we see potential in using the federation to provide more flexibility in the …

Suddenly...I'M Consulting On Data Management Plans! Data Management Plan Consultant Checklist, Kiyomi D. Deards

University of Nebraska-Lincoln Libraries: Presentations

This webinar will outline the most important questions to ask, and the best resources available, for those who "suddenly" will be consulting on data management plans.

Segmenting Tables Via Indexing Of Value Cells By Table Headers, Sharad C. Seth, George Nagy

School of Computing: Conference and Workshop Papers

Correct segmentation of a web table into its component regions is the essential first step to understanding tabular data. Our algorithmic solution to the segmentation problem relies on the property that strings defining row and column header paths uniquely index each data cell in the table. We segment the table using only “logical layout analysis” without resorting to any appearance features or natural language understanding. We start with a CSV table that preserves the 2- dimensional structure and contents of the original source table (e.g., an HTML table) but not font size, font weight, and color. The indexing property of …

Data Mining The Functional Characterizations Of Proteins To Predict Their Cancer-Relatedness, Peter Revesz, Christopher Assi

School of Computing: Faculty Publications

This paper considers two types of protein data. First, data about protein function described in a number of ways, such as, GO terms and PFAM families. Second, data about whether individual proteins are experimentally associated with cancer by an anomalous elevation or lowering of their expressions within cancerous cells. We combine these two types of protein data and test whether the first type of data, that is, the functional descriptors, can predict the second type of data, that is, cancer-relatedness. By using data mining and machine learning, we derive a classifier algorithm that using only GO term and PFAM family …

Biodiversity Heritage Library, Smithsonian Institution Libraries, Deanna Marcum

Copyright, Fair Use, Scholarly Communication, etc.

The Biodiversity Heritage Library (BHL), created in 2006, is the result of a collaboration of ten natural history museum and botanical garden libraries seeking to digitize core taxonomic literature and to make it free and openly available throughout the world. Today, the BHL includes fifteen member institutions whose efforts have shaped a collection of over 60,000 titles. It is supported through a combination of membership dues, in-kind support from member institutions, contributions from the user community, and direct support from the Smithsonian Institution Libraries, and it reaches tens of thousands of users each year. While managing the complex partnership has …

Data Mining Of Pancreatic Cancer Protein Databases, Peter Revesz, Christopher Assi

School of Computing: Conference and Workshop Papers

Data mining of protein databases poses special challenges because many protein databases are non- relational whereas most data mining and machine learning algorithms assume the input data to be a type of rela- tional database that is also representable as an ARFF file. We developed a method to restructure protein databases so that they become amenable for various data mining and machine learning tools. Our restructuring method en- abled us to apply both decision tree and support vector machine classifiers to a pancreatic protein database. The SVM classifier that used both GO term and PFAM families to characterize proteins gave …

Data Mining Of Protein Databases, Christopher Assi

School of Computing: Dissertations, Theses, and Student Research

Data mining of protein databases poses special challenges because many protein databases are non-relational whereas most data mining and machine learning algorithms assume the input data to be a relational database. Protein databases are non-relational mainly because they often contain set data types. We developed new data mining algorithms that can restructure non-relational protein databases so that they become relational and amenable for various data mining and machine learning tools. We applied the new restructuring algorithms to a pancreatic protein database. After the restructuring, we also applied two classification methods, such as decision tree and SVM classifiers and compared their …

An Approach To The Virtual Flora Of Mongolia – From A Data Repository To An Expert System, Http://Greif.Uni-Greifswald.De/Floragreif/, Jörg Hartleib, Martin Schnittler, Sabrina Rilke, Anne Zemmrich, Bernd Bobertz, Ulrike Najmi, Reinhard Zölitz, Susanne Starke

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

FloraGREIF is an internet accessible information system providing taxonomic, phytogeographic and ecological information on Mongolia’s flora in terms of descriptions, high-resolution plant images and an interactive WebGIS application. Organised along an updated checklist of the approx. 3000 Mongolian vascular plants that serves as a taxonomic backbone, information is split into the taxon level, referring to plant species, and the record level, referring to record or a collected plant specimen. At the latter level, images of living plants, scans of herbarium sheets, habitat photos and further notes can be found. Both data levels are linked by the name of the respective …

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

Department of Computer Electronics and 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 …

Applying Data Mining Techniques To Evaluate Applications For Agricultural Loans, Emile J. Salame

Department of Agricultural Economics: Dissertations, Theses, and Student Research

Financial lending institutions continuously look at improving their credit risk models. This study examines the performance of three estimation methods: logistic regression, decision tree, and neural networks, in terms of their misclassification rates of credit default. The study uses 17,328 loans of grain producers for the period of 2006 - 2010. Those loans belong to the category of “diversified loans / core standard” originating from a large financial lending institution. The data has been split into nine different sets to acknowledge three factors: the shift in price of grains to a higher plateau after 2006, the contamination effect on defaulting …

Propeller: A Scalable Metadata Organization For A Versatile Searchable File System, Lei Xu, Hong Jiang, Xue Liu, Lei Tian, Yu Hua, Jian Hu

School of Computing: Technical Reports

The exponentially increasing amount of data in file systems has made it increasingly important for users, administrators and applications to be able to fast retrieve files using file-search services, instead of replying on the standard file system API to traverse the hierarchical namespaces.  The quality of the file-search services  is significantly affected by the file-indexing overhead, the file-search performance and the accuracy of search results.  Unfortunately, the existing file-search solutions either are so poorly scalable that their performance degrades unacceptably when the systems scale up, or incur so much crawling delays that they produce acceptably inaccurate results.  We believe that …

Rapport: Semantic-Sensitive Namespace Management In Large-Scale File Systems, Yu Hua, Hong Jiang, Yifeng Zhu, Dan Feng

School of Computing: Technical Reports

Explosive growth in volume and complexity of data exacerbates the key challenge to effectively and efficiently manage data in a way that fundamentally improves the ease and efficacy of their use. Existing large-scale file systems rely on hierarchically structured namespace that leads to severe performance bottlenecks and renders it impossible to support real-time queries on multi-dimensional attributes. This paper proposes a novel semantic-sensitive scheme, called Rapport, to provide dynamic and adaptive namespace management and support complex queries. The basic idea is to build files’ namespace by utilizing their semantic correlation and exploiting dynamic evolution of attributes to support namespace management. …

Genbank, Dennis A. Benson, Ilene Karasch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers

Harold W. Manter Laboratory of Parasitology: Library Materials

GenBank(R) is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data …

Temporal Data Classification Using Linear Classifiers, Peter Revesz, Thomas Triplet

School of Computing: Conference and Workshop Papers

Data classification is usually based on measurements recorded at the same time. This paper considers temporal data classification where the input is a temporal database that describes measurements over a period of time in history while the predicted class is expected to occur in the future. We describe a new temporal classification method that improves the accuracy of standard classification methods. The benefits of the method are tested on weather forecasting using the meteorological database from the Texas Commission on Environmental Quality.

Using Gis To Locate Areas For Growing Quality Coffee In Honduras, Ellen Mickle

Department of Environmental Studies: Undergraduate Student Theses

Abstract Small-scale coffee producers worldwide remain vulnerable to price fluctuations after the 1999-2003 coffee crisis. One way to increase small-scale farmer economic resilience is to produce a more expensive product, such as quality coffee. There is growing demand in coffee-producing and coffee-importing countries for user-friendly tools that facilitate the marketing of quality coffee. The purpose of this study is to develop a prototypical quality coffee marketing tool in the form of a GIS model that identifies regions for producing quality coffee in a country not usually associated with quality coffee, Honduras. Maps of areas for growing quality coffee were produced …

Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson

School of Computing: Conference and Workshop Papers

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSN- PSSM), which uses all the information in the entire ToF- SIMS …

Getting Started With Prpl, Qingfeng Guan

School of Natural Resources: Faculty Publications

pRPL is an open-source1 general-purpose parallel Raster Processing programming Library developed by Qingfeng Guan, in the Department of Geography, University of California, Santa Barbara. pRPL encapsulates complex parallel computing utilities and routines specifically for raster processing (e.g., raster data decomposition, distribution and gathering among multiple processors, inter-processor communication and data exchange), and provides an easy-to-use interface for users to parallelize almost any raster processing algorithm with any arbitrary neighborhood (or moving window) configuration. pRPL enables the implementation of parallel raster-processing algorithms without requiring a deep understanding of parallel computing and programming, thus it greatly reduces the development complexity. Moreover, even …

Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao

School of Computing: Dissertations, Theses, and Student Research

Spatiotemporal datasets can be classified into two categories: temporal-oriented and spatial-oriented datasets depending on whether missing spatiotemporal values are closer to the values of its temporal or spatial neighbors. We present an adaptive spatiotemporal interpolation model that can estimate the missing values in both categories of spatiotemporal datasets. The key parameters of the adaptive spatiotemporal interpolation model can be adjusted based on experience.

Intelligent Resource Discovery Using Ontology-Based Resource Profiles, J. Steven Hughes, Dan Crichton, Sean Kelly, Chris A. Mattmann, Jerry Crichton, Thuy Tran

Copyright, Fair Use, Scholarly Communication, etc.

Successful resource discovery across heterogeneous repositories is highly dependent on the semantic and syntactic homogeneity of the associated resource descriptions in each repository. Ideally, consistent resource descriptions are easily extracted from each repository, expressed using standard syntactic and semantic structures, and managed and accessed within a distributed, flexible, and scalable software framework. In practice however, seldom do all three of these elements exist. To help address this situation, the Object Oriented Data Technology (OODT) project at the Jet Propulsion Laboratory has developed an extensible, standards-based resource description scheme that provides the necessary description and management facilities for the discovery of …

Comparison Of Modis And Avhrr 16-Day Normalized Difference Vegetation Index Composite Data, Kevin P. Gallo, Lei Ji, Brad Reed, John Dwyer, Jeffrey Eidenshink

School of Natural Resources: Faculty Publications

Normalized difference vegetation index (NDVI) data derived from visible and near-infrared data acquired by the MODIS and AVHRR sensors were compared over the same time periods and a variety of land cover classes within the conterminous USA. The relationship between the AVHRR derived NDVI values and those of future sensors is critical to continued long term monitoring of land surface properties. The results indicate that the 16-day composite values are quite similar over the 23 intervals of 2001 that were analyzed, and a linear relationship exists between the NDVI values from the two sensors. The composite AVHRR NDVI data were …

Digitization In An Archival Environment, Sally Mckay

E-JASL: Electronic Journal of Academic and Special Librarianship (1999-2009, Volumes 1-10)

Introduction

Cultural institutions such as museums, libraries, archives, and historical societies house remarkable collections of cultural artifacts. It is the responsibility of the staff working for those institutions to preserve, protect and provide responsible stewardship for the materials, and to the best of their ability, provide continued long-term access (Russell, 2000).

Advances in technology allow institutions to provide expanded access and education; however, there are important priorities that must be addressed prior to embarking on a digital conversion project.

Digitization in an archival environment includes taking a physical object or analog item, such as an art object, a tape recording, …

Cataloging Expert Systems: Optimism And Frustrated Reality, William Olmstadt

E-JASL: Electronic Journal of Academic and Special Librarianship (1999-2009, Volumes 1-10)

There is little question that computers have profoundly changed how information professionals work. The process of cataloging and classifying library materials was one of the first activities transformed by information technology. The introduction of the MARC format in the 1960s and the creation of national bibliographic utilities in the 1970s had a lasting impact on cataloging. In the 1980s, the affordability of microcomputers made the computer accessible for cataloging, even to small libraries. This trend toward automating library processes with computers parallels a broader societal interest in the use of computers to organize and store information. Following World War II, …

The Computer As A Collection Management Tool, Suzanne B. Mclaren, Hugh H. Genoways, Duane A. Schlitter

University of Nebraska State Museum: Mammalogy Papers

Since the mid-1960s, discussion of computer use for information retrieval in museum collections has usually focused on research potential. Much attention has been given to the idea of networking and the ability to access data across great distances. However, the potential for collection management usage has also proven to be a legitimate rationale for computerization. Numerous aspects of collection management are discussed for which the computer may be employed. Topics include creating cross-reference files, updating taxonomic and geographic information, pinpointing mismatched specimens, locating lost and uncataloged material, controlling loan procedures, producing accession files for insurance purposes, curating all or part …