Database Integration

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.

Extraction-Transformation-Loading (ETL) tools are pieces of software responsible for the extraction of data from several sources, their cleansing, customization, and insertion into a data warehouse. In this paper, we delve into the logical optimization of ETL processes, modeling it as a state-space search problem. We consider each ETL workflow as a state and fabricate the state space through a set of correct state transitions. Moreover, we provide an exhaustive and two heuristic algorithms toward the minimization of the execution cost of an ETL workflow. The heuristic algorithm with greedy characteristics significantly outperforms the other two algorithms for a large set of experimental cases.

Resolving domain incompatibility among independently developed databases often involves uncertain information. DeMichiel (1989) showed that uncertain information can be generated by the mapping of conflicting attributes to a common domain, based on some domain knowledge. The authors show that uncertain information can also arise when the database integration process requires information not directly represented in the component databases, but can be obtained through some summary of data. They therefore propose ...

A federated database system (FDBS) is a collection of cooperating database systems that are autonomous and possibly heterogeneous. In this paper, we define a reference architecture for distributed database management systems from system and schema viewpoints and show how various FDBS architectures can be developed. We then define a methodology for developing one of the popular architectures of an FDBS. Finally, we discuss critical issues related to developing and operating an FDBS.

This study developed and implemented an improved mediator wrapper approach to addressing the challenges of integration of semantic heterogeneous databases. It employed Local as View (LaV) paradigm of database integration so as to reduce its cost as well as offer the local sources a degree of independence. The developed model was implemented as web service using JEE and some software development tools with a number of heterogeneous databases as a case study.

Database security concerns the use of a broad range of information security controls to protect databases against compromises of their confidentiality, integrity and availability. Data integrity, in turn, is a fundamental component of information security. It refers to the accuracy and consistency of data stored in a database, data warehouse, data mart or other constructs. This tutorial provides an overview of data Integrity issues (such as, concurrency control),  and database security issues and the role of database administrator.

Claims and disputes on time extension for delays are common in construction projects. Various methods and divergent approaches are used by different parties in assessing delays. Disputes then often arise on (a) eligibility of a delay event for claiming extension of time (EOT), (b) choice of method for evaluating EOT, and (c) quantification of the EOT. This research initiative aims at formulating a knowledge-based decision guidance system to help all concerned parties in navigating through these various options, in order to rationalize their approaches towards the preparation and evaluation of the EOT claims. Such rationalization is based on structured approaches, which are in turn devised from the particular contractual and project conditions. This rationalization is also expected to assist in a convergence of assessment approaches that would in turn reduce disputes and consequently wasted resources. In targeting those aims, a prototype of an integrated decision support system (DSS) for dealing with time extension claims was recently developed using (a) a structured web-based decision support framework, which is supplemented by (b) a Pocket PC based portable framework with seamless database integration. This paper presents some essential highlights on the development and usefulness of key modules of the DSS.

In the last decades, the use of ontologies in information systems has become more and more popular in various fields, such as web technologies, database integration, multi agent systems, natural language processing, etc. Artificial intelligent researchers have initially borrowed the word “ontology” from Philosophy, then the word spread in many scientific domain and ontologies are now used in several developments.

A database integrating 90 years of empirical studies reporting intercorrelations among rated job performance dimensions was used to test the hypothesis of a general factor in job performance. After controlling for halo error and 3 other sources of measurement error, there remained a general factor in job performance ratings at the construct level accounting for 60% of total variance. Construct-level correlations among rated dimensions of job performance were substantially inflated by halo for both supervisory (33%) and peer (63%) intrarater correlations These findings have important implications for the measurement of job performance and for theories of job performance.

Wireless local area network (WLAN) has been widely used in many sectors. The popularity gained is due to many reasons, such as ease of installation, installation flexibility, mobility, reduced cost-of-ownership, and scalability. However, regardless of the benefits mentioned above, WLAN have some security threats, in which anyone who use it or intend to use it should be aware. This paper begins by introducing the concept of WLAN. The introductory section gives brief information on the WLAN components and its architecture. In order to examine the WLAN security threats, this paper will look at Denial of Service, Spoofing, and Eavesdropping. This paper will also tell about the reasons of loss of data and the security measures that are involved to reduce the loss of data from hackers by using the data confidentiality and prevention and access control mechanism.

Every scientist knows that research results are only as good as the data upon which the conclusions were formed. However, most scientists receive no training in methods for achieving, assessing, or controlling the quality of research data— topics central to clinical research informatics. This chapter covers the basics of collect and process research data given the available data sources, systems, and people. Data quality dimensions specifi c to the clinical research context are used, and a framework for data quality practice and planning is developed. Available research is summarized, providing estimates of data quality capability for common clinical research data collection and processing methods. This chapter provides researchers, informaticists, and clinical research data managers basic tools to plan, achieve, and control the quality of research data.

One of the fundamental principles of the database approach is that a database allows a nonredundant, unified representation of all data managed in an organization. This is achieved only when methodologies are available to support integration across organizational and application boundaries.

State-of-the-art OLTP systems execute distributed transactions using XA-2PC protocol, a presumed-abort variant of the Two-Phase Commit (2PC) protocol. While the XA specification provides for the Read-Only and 1PC optimizations of 2PC, it does not deal with another important optimization, coined Nested 2PC. In this paper, we describe the Logging Last Resource (LLR) optimization in Oracle WebLogic Server (WLS). It adapts and improves the Nested 2PC optimization to/for the Java Enterprise Edition (JEE) environment. It allows reducing the number of forced (synchronous) writes and the number of exchanged messages when executing distributed transactions that span multiple transactional resources including a SQL database integrated as a JDBC datasource. This optimization has been validated in SPECjAppServer2004 (a standard industry benchmark for JEE) and a variety of internal benchmarks. LLR has been successfully deployed by high-profile customers in mission-critical highperformance applications.

Inductive databases integrate database querying with database mining. In this article, we present an inductive database system that does not rely on a new data mining query language, but on plain SQL. We propose an intuitive and elegant framework based on virtual mining views, which are relational tables that virtually contain the complete output of data mining algorithms executed over a given data table. We show that several types of patterns and models that are implicitly present in the data, such as itemsets, association rules, and decision trees, can be represented and queried with SQL using a unifying framework. As a proof of concept, we illustrate a complete data mining scenario with SQL queries over the mining views, which is executed in our system.

A federated database system (FDBS) is a collection of cooperating database systems that are autonomous and possibly heterogeneous. In this paper, we define a reference architecture for distributed database management systems from system and schema viewpoints and show how various FDBS architectures can be developed. We then define a methodology for developing one of the popular architectures of an FDBS. Finally, we discuss critical issues related to developing and operating an FDBS.

Corporate databases are potentially rich sources of new and valuable knowledge. Various approaches to "discovering" or "mining" such knowledge have been proposed. We identify an important and previously ignored discovery task, data archaeology. Data archaeology is a skilled human task, in which the knowledge sought depends on the goals of the analyst, cannot be specified in advance, and emerges only through an iterative process of data segmentation and analysis. We describe a system that supports the data archaeologist with a natural, objectoriented representation of an application domain; a powerful query language and database translation routin~s; and an easy-to-use and flexible user interface that supports interactive exploration. A formal knowledge representation system provides the core technology that facilitates database integration, querying, and the reuse of queries and query results.

We present a data model for the initial implementation of MetPetDB, a geochemical database specific to metamorphic rock samples. The database is designed around the concept of preservation of spatial relationships, at all scales, of chemical analyses and their textural setting. Objects in the database (samples) represent physical rock samples; each sample may contain one or more subsamples with associated

We address the problem of providing integrated access to diverse and dynamic information sources. We explain how this problem di ers from the traditional database integration problem and we focus on one aspect of the information integration problem, namely information exchange. We de ne an object-based information exchange model and a corresponding query language that we believe are well suited for integration of diverse information sources. We describe how the model and language have been used to integrate heterogeneous bibliographic information sources. We also describe two general-purpose libraries we have implemented for object exchange between clients and servers.

Database integration provides integrated access to multiple data sources. Database integration has two main activities: schema integration (forming a global view of the data contents available in the sources) and data integration (transforming source data into a uniform format). This paper focuses on automating the aspect of data integration known as entity identification using data mining techniques. Once a global database is formed of all the transformed source data, there may be multiple instances of the same entity, with different values for the global attributes, and no global identifier to simplify the process of entity identification. We implement decision trees and k-NN as classification techniques, and we introduce a preprocessing step to cluster the data using conceptual hierarchies. We conduct a performance study using a small testbed and varying parameters such as training set size and number of unique entities to study processing speed and accuracy tradeoffs. We find th...

Abstract. Russian social science studying the public opinion has accumulated considerable datasets of research data obtained over the past 25 years. In theory, the quantitative data growth is to be transferred into the emergence of qualitatively new insights. But this does not happen, because the following use of the research data is problematic due to huge number methodologies and unresolved problems of measurement. Qualitatively new heuristic capabilities of big data complicate the situation. The article discusses the problems of data bases integration of diverse sociological studies into a single data environment.
Аннотация. В российской социологии общественного мнения накоплено множество массивов исследований, проведенных за последние 25 лет. В теории количественный прирост данных должен выливаться в появление качественно новых инсайтов. Но этого не происходит, т.к. их вторичное использование в силу «методологического анархизма» и нерешенных проблем измерения является проблематичным. Усложняет ситуацию появление больших данных с качественно новыми эвристическими возможностями. В статье обсуждаются проблемы объединения баз данных разнородных социологических исследований в единой среде. Ключевые слова: социология общественного мнения, социологическая история, база данных, объединение баз данных, шкала, онтология, онтологический словарь.

A key problem in providing 'enterprise-wide' information is the integration of databases that have been independently developed. An important requirement is to accommodate heterogeneity and maintain the autonomy of component databases. Myriad is a federated database prototype developed at the University of Minnesota, to provide a testbed for investigating alternatives in architecture and algorithms for database integration, query processing and optimization, and concurrency control and recovery. The system incorporates our group's research results in these areas. This paper describes our experiences in the design and implementation of Myriad, and in the project management. Special emphasis is given to discussing design alternatives and their impact on Myriad. This paper also presents the software engineering principles and the project management techniques we used in developing Myriad and the lessons we learned. We believe these lessons would be useful for practitioners who wish to develop a similar system.

x Our comments about the paper by Leeflang and Wittink Internat. J. Res. Marketing, 17 2000 105 comprise of two components: first, we address two issues on which we disagree with Leeflang and Wittink: soft versus hard data, and individual-level versus segment-level models. Secondly, we supplement their paper by attempting to predict how marketing model building will change in the future. q

The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.

Schema integration is important in two contexts, logical database design (in centralized DBMS) and global schema design (in distributed DBMS). Performing an integration on real-life schemas without a tool can be very difficult, tedious and error prone. We have developed an interactive tool to assist database designers and administrators (DDA) in integrating schemas. It collects the information required for integration from a DDA, performs essential bookkeeping, and integrates schemas according to the semantics provided. This paper presents the capabilities of this tool by discussing
the integration methodology and the user interface of the tool.

Keywords: schema integration, view integration, database design and integration, conceptual data model, ECR model, interactive tool,
database designer and administrator

Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach a b s t r a c t Global control of tuberculosis is increasingly dependent on rapid and accurate genetic typing of Mycobacterium tuberculosis. Spoligotyping is a first-line genotypic fingerprinting method for M. tuberculosis isolates. An international online database (SpolDB4) of spoligotype patterns has been established wherein a clustered pattern (shared by 2 isolates) is designated a shared international type (SIT). Dual infections of single patients by distinct strains of M. tuberculosis is increasingly reported in high tuberculosis incidence areas, raising the possibility of false composite spoligotype patterns if performed upon mixed strain samples. A computational approach was applied to SpolDB4 and found that of the reported 1939 SITs, 54% could be a composite of two other SITs. Although many of the spoligotypes listed in SpolDB4 may be the product of admixing, the majority of patterns were reported with a corresponding low case frequency and so the effect of misclassification upon database integrity with these is likely minimal. Phylogenetic analysis of the five SITs most prone to be a composite demonstrated that these patterns designate nodes from which the ramifications of large families T, MANU, LAM, and EAI emerged. We illustrate how geographic context may indicate when an observed pattern could be the product of mixed infection. Importantly, when one of the most composite-prone SITs is obtained, further genetic testing by alternate methods is prudent to rule-out mixed infection, especially in high tuberculosis prevalence areas. These findings have broad practical implications for tuberculosis control and surveillance, as well as highlight the utility of a computational approach in providing solutions to biological questions in which the information can be digitalized. j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m e e g i d 2.2. SpolDB4 database The SpolDB4 database created and maintained by the Pasteur Institute of Guadeloupe (Brudey et al., 2006) is available online (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo); the publicly available version contains 1939 SITs corresponding to 35,925 strains, as well as 3370 orphan patterns, from 121 countries. The five most common M. tuberculosis spoligotypes in this database were SIT53 (T1), SIT1 (Beijing), SIT50 (Haarlem3), SIT42 (LAM9) and SIT47 (Haarlem1).

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classi®cations that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Ontology is presently an emerging research topic in the field of artificial intelligence, semantic web, and natural language processing, software engineering, and information architecture etc. Manual Ontology building is essentially a time consuming and tedious task. From the last few decades, different ontology building approaches are being used to build ontology either semi-automatically or automatically. This paper review has been carried out/done on the usage of different ontology building approaches in natural language processing and their usage on Indian languages. It is hereby concluded from the review that in Indian languages usage of ontology is very less because of the challenges to build ontology for minority languages.

Biological data sources are known for its heterogeneous in many aspects. These aspects include data formats, physical location as well as its query capabilities. These data sources need to be integrated so that researchers can easily access it, query it and get results. Approaches like link-driven, data warehousing and mediatorbased are being used to integrate these data sources. This paper tries to look at the dissimilarities of major biological data sources and some major approaches in dealing with the biological multi-database integration. Mediator based with ontologies approach is also discussed in this paper. Proposed work on merging biology ontologies in a mediated system is also presented.

The actual value of the Deep Web comes from integrating the data its applications provide. Such applications offer human-oriented search forms as their entry points, and there exists a number of tools that are used to fill them in and retrieve the resulting pages programmatically. Solution that rely on these tools are usually costly, which motivated a number of researchers to work on virtual integration, also known as metasearch. Virtual integration abstracts away from actual search forms by providing a unified search form, i.e., a programmer fills it in and the virtual integration system translates it into the application search forms. We argue that virtual integration costs might be reduced further if another abstraction level is provided by issuing structured queries in high-level languages such as SQL, XQuery or SPARQL; this helps abstract away from search forms. As far as we know, there is not a proposal in the literature that addresses this problem. In this paper, we propose a reference framework called IntegraWeb to solve the problems of using high-level structured queries to perform deep-web data integration. Furthermore, we provide a comprehensive report on existing proposals from the database integration and the Deep Web research fields, which can be used in combination to address our problem within the previous reference framework.

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. For this purpose our ontology offers a variety of distinct partitions -of substances, processes and functions -and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GO TM , KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration.

I1 High-throughput next generation sequencing technologies foster new computing techniques in bioinformatics Mary Qu Yang et al. S1 Prediction of DNA-binding residues from protein sequence information using random forests Liangjiang Wang et al. S2 Reconstruct gene regulatory network using slice pattern model Yadong Wang et al. S3 Comparison of feature selection and classification for MALDI-MS data Qingzhong Liu et al. S4 Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing Xin Wang et al. S5 Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse Elsa Chacko and Shoba Ranganathan S6 Annotating the human genome with disease ontology John D Osborne et al.

This paper describes the objectives and goals of the FEMUS project, a joint research project of the database research groups at EPF Lausanne and ETH Zürich. It presents an overview on FEMUS and the first results on comparison between ERC+ and COCOON.

The paper presents the results of a trilateral research project carried out jointly by German, Israeli, and Palestinian institutions. The overall objective of the project was to develop and adapt models and tools for resource-preserving transport planning in the West Bank and the adjacent areas. Because of its high dynamics and the particular political circumstances, broader socioeconomic and political considerations needed to be included in the analysis of present conditions and the exploration of future developments in this area. Compared to other countries, transport planning in Palestine is much more linked to sensitive issues such as security, Israeli settlements, bypass roads and checkpoints, which cannot always be separated in a clean way. To evaluate different policy options for transport planning, a modelling system has been developed consisting of a GIS database, integrated transport and environmental models and network extensions tools. The paper presents the integrated database and the modelling system developed, describes the scenarios implemented and compares the outcomes of the model runs with respect to their environmental and social impacts.

Database integration is currently solved only for the case of simple structures. Semantics is mainly neglected. It is known but often neglected that database integration cannot be automated. System integration is far more difficult. Both integrations can only be performed if a number of assumptions can be made for the integrated system. Instead of integrating systems entirely cooperation or collaboration of systems can be developed and used. We propose in this paper the extension of the view cooperation approach to database collaboration.

As mobile ad hoc networks (MANETs) are becoming popular for a variety of applications, so are the issues surrounding corresponding implementations. In this paper, a healthcare application is developed for an environment where normal network connectivity may not be available hence networking of small scale healthcare units and corresponding devices becomes necessary. Different roles of such units are discussed to facilitate role based access control (RBAC) conformant access. The concepts of role-based access and databases are combined to specify separation of duty (on ad hoc networks) as required for database integrity. The framework to adapt policy based access control model in the MANET environment is discussed. Furthermore, XML implementation of such access control within a typical rural healthcare environment is investigated.

Today, databases provide the best technique for storing and retrieving data, but they suffer from the absence of a semantic perspective, which is needed to reach global goals such as the semantic web and data integration. Using ontologies will solve this problem by enriching databases semantically. Since building an ontology from scratch is a very complicated task, we propose an automatic transformation system to build Web Ontology Language OWL ontologies from a relational model written in Structured Query Language SQL. Our system also uses metadata, which helps to extract some semantic aspects which could not be inferred from the SQL. Our system analyzes database tuples to capture these metadata. Finally, the outcome ontology of the system is validated manually by comparing it with a conceptual model of the database (E/R diagram) in order to obtain the optimal ontology.

The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies.