Integrating life science Web databases, while important and necessary, is a challenge for current integration systems mainly due to the large number of these databases, their heterogeneity and the fact that their interfaces may change often. BACIIS, a biological and chemical information integration system, is a tightly coupled federated database system that uses the mediator wrapper method in order to retrieve information from several remote Web databases. BACIIS relies on a semi-automated approach for generating and maintaining wrappers in order to provide a scalable system with a limited maintenance overhead. The semi-automatic wrapper induction in BACIIS is efficient because it is based on, but not limited to a domain knowledge. Tests show that the use of ontology increases the accuracy of the wrapper induction. We also present how the wrapper induction system facilitates wrapper update, and assists in the information extraction. By using a wrapper induction system for creation and maintenance of wrappers, scalability, flexibility, and stability of the integrated information system is easily maintained.

Life science Web databases are becoming increasingly essential in conducting everyday biological research. With more than 300 life science Web databases and the growing size of the life science data, searching and managing these complex data requires technology beyond that of traditional database systems. The open research issues include the interoperability of geographically distributed autonomous databases, which are generally only Web-accessible, and the seamless semantic-based integration of these databases with total transparency to the user. In this paper, the implementation of a Biological and Chemical Information Integration System (BACIIS) is presented. BACIIS supports the integration of multiple heterogeneous life science Web databases and allows the execution of global applications that extend beyond the boundaries of individual databases. This paper discusses the architecture of BACIIS. It also discusses the techniques used to extract and integrate data from the various life science Web databases.

Modern biological studies rely on life science Web databases as well as sophisticated Web-based software tools (e.g., homology search tools, modeling and visualization tools). These tools or Web services often have to be combined and integrated in order to support a given study (i.e. an in-silico experiment). The large number of the available Web services makes a service discovery process that can identify the set of services that satisfy a given number of constraints from the pool of all the available Web services crucial. Without such an automated service discovery process the user will have to have a thorough knowledge of all of the existing Web services, a task-which is impractical in the life science domain. In this paper, a scalable approach to service discovery in the biological domain is presented. The approach is based on and guided by a domain ontology.

In the past decade chemical and biological laboratory experiments have generated an explosive amount of data. As a result, a set applications that manipulate these dynamic, heterogeneous and massive amounts of data have emerged. An example of such applications in the pharmaceutical industry is the computational process involved in the early drug discovery of lead drug candidates for a given target disease. The discovery of lead drug candidates requires both consecutive and random data access to the pharmaceutical drug candidate database. This paper focuses on performance enhancement techniques for the pharmaceutical drug candidate database application. In particular, this paper compares static load balancing and dynamic load balancing in the context of the drug candidate database application. This database application is based on multi-queries. Some of these queries are multi-join queries.

The Global Change Master Directory (GCMD) is an Earth science information repository that specifically tracks research data on global climatic change. Building a directory of Earth science metadata that allows the exchange of metadata content among partner organizations is challenging due to the complex issues involved in supporting heterogeneous metadata schema, database schema, database implementation and platforms. This demonstration presents the design of the MD8 (Master Directory v8.0), which allows automated exchange of metadata content among Earth science collaborators through a proposed asynchronous distributed transaction protocol. Specifically, the demonstration focuses on the local data agent that captures local database updates and broadcasts them to other cooperating nodes asynchronously using an announcer.

Recent advances in the development of new, high throughput screening technologies have resulted in a wealth of life science data. The complexity and volume of these data require technology beyond that of traditional database systems. Open research issues include the seamless, semantic-based integration of geographically distributed, autonomous web databases. Biological And Chemical Integration Information System (BACIIS) addresses these issues. This paper discusses the challenges associated with the integration of life science web databases and the techniques used in BACIIS to address these challenges. Particularly, the execution of life science, multidatabase queries is investigated, and an approach that can overcome the limitations of the query capabilities of each individual life science web database participating in the integration is presented. This approach hides the heterogeneity of the individual databases from the user while providing an efficient execution plan for complex, life science, multidatabase queries.

Recently, technological advances in digital imaging modalities and high-speed networks have enabled physicians to store digital medical images and integrate them with the patient's electronic medical record for fast access by computer. This paper outlines the characteristics and design requirements of an image workflow management system (IWFMS) in a large-scale hospital environment. In this paper, we present a four-tiered enterprise architecture of an IWFMS for supporting the streamlining, automating and monitoring of the flow of the medical images in a large-scale consortium of hospitals known as the Clarian Health System in Indianapolis, IN, USA. The first tier presents the graphical user interface (GUI) that enables users to view and interact with the workflow engine. The second tier implements the business model that depends on the work requirements within the different units of the hospital system. The third tier implements the business logic and automates tasks that support image flows. The fourth tier is the back-end database that is used to store and retrieve workflow data. The components in each tier have been designed and implemented as a set of CORBA objects that provide seamless integration of the image flows in the Clarian Health System.

Large scientific databases often consist of heterogeneous components that differ in the number of attributes and the number of tuples. In this paper, we show that increased performance is achieved when a complex schema is used to represent different components of a data repository. The driving application used in this study is a pharmaceutical drug repository. The types of access patterns associated with this repository consist of the retrieval of a selected set of attribute values for a consecutive or a random set of tuples. These consecutive and random access patterns, which are typical of a drug discovery experiment, are used to measure the data retrieval throughput for different schemas.

An explosion in the amount of data generated through chemical and biological experimentation has been observed in recent years. This rapid proliferation of vast amounts of data has led to a set of cheminformatics and bioinformatics applications that manipulate dynamic, heterogeneous, and massive data. An example of such applications in the pharmaceutical industry is the computational process involved in the early discovery of lead drug candidates for a given target disease. This computational process includes repeated sequential and random accesses to a drug candidate database. Using the above pharmaceutical application, an experimental study was conducted in this paper that shows that for optimal performance, the degree of parallelism exploited in the application should be adjusted according to the drug candidate database instance size and the machine size. Additionally, different degrees of parallelism should be used depending on whether the access to the drug candidate database is random or sequential.

Although satellite and cellular communication advances have enabled users of mobile computers the ability to access information regardless of location, it introduces new problems for transaction management in distributed database systems. Traditional transaction mechanisms and criteria have to be adjusted to accommodate the limitations of a mobile computing environment. Data replication is an example of a technique that is used in traditional database systems to increase the availability and the fault-tolerance of the data, but at the same time adds the overhead of maintaining replica consistency across multiple sites of the network. Data replication is a useful tool in mobile computing due to the fact that a mobile host may be disconnected from the network for long periods of time. The data replication allows the mobile host to use a local data copy while it is disconnected from the network. Mobile hosts that have the capability to store copies of data items increase the difficulty of maintaining replica consistency, because of the mobile host's volatile storage. Also, the mobile host must be assured that the local copies that it is using are valid, and any changes made locally to a copy are reflected in the rest of the system. We introduce a mobile replica management algorithm. A mobile transaction manager (MTM) coordinates the transactions initiated by mobile hosts, which query and update replicated databases stated at both mobile and static hosts in a battlefield environment. This battlefield environment is based upon the U.S. telemedicine (Prime Time III) support in Bosnia. The MTM is responsible for the synchronization of the replicated data items in the network.

Develops a formal basis for research into the reliability aspects of transaction processing in multidatabase systems (MDBSs). We define a new correctness notion called 'global committability' for the correct unilateral commit and the retry recovery of global transactions in an autonomous MDBS environment. This notion makes it easier to ensure the isolation property of global transactions when the retry approach is applied. The formalization work illustrates that the conventional serializability and recoverability notions are not sufficient to specify the correct execution (i.e. isolated execution and recovery) of global transactions when the unilateral commit and the retry recovery are used to ensure the atomicity of global transactions. This work is significant because the unilateral commit and the retry recovery are an attractive complementary means to the undo recovery (whose correct schedule is specified by the conventional recoverability notion) for advanced transaction applications with the characteristics of site autonomy and long-lived execution.

In a mobile computing environment, a user carrying a portable computer can execute a mobile tmnsaction by submitting the operations of the transaction to distributed data servers from different locations.As a result of this mobility, the operations of the transaction may be executed at different servers.The distribution of operations implies that the transmission of messages (such as those involved in a two phase commit protocol) may be required among these data servers in order to coordinate the execution of these operations.In this paper, we will address the distribution of operations that update partitioned data in mobile environments.We introduce a new algorithm, the Reservation Algorithm (RA), that does not necessitate the incurring of message overheads (e.g., for a 2PC protocol) for operations pertaining to resource allocation.We address one related issue, termination protocols, which guarantees that the commit decision of a mobile host will not contradict with the unilateral abort decision of a data server.

We present a new lock management scheme which allows a read unlock for an item to be executed at any copy site of that item; the site may be different from the copy site on which the read lock is set. The scheme utilizes the replicated copies of data items to reduce the message costs incurred by the mobility of the transaction host. We demonstrate this idea in an optimistic locking algorithm called O2PL-MT (Optimistic Two Phase Locking for Mobile Transactions). Like its counterpart algorithm O2PL (Optimistic Two Phase Locking), O2PL-MT grants read locks immediately on demand and defers write locks until the commitment time. However, O2PL-MT requires the transmission of fewer messages than O2PL in a mobile environment in which data items are replicated.

Discusses issues related to the design and and usage of database management systems consisting of massive amounts of data in parallel environments. The issues include the placement of the data in the memory, file systems, concurrent access to data, effects on query processing, the implications of specific machine architectures, and the peculiarities of specific parallel systems. Since not all parameters are currently amenable to rigorous analysis, results of performance studies are highlighted wherever they are deemed appropriate. >

The paper presents two protocols for maintaining consistency of replicated data in multidatabase systems. The protocols meet both autonomy and consistency requirements by employing different replica control and commitment approaches: unilateral local commitment and deferred propagation for local applications, and two-phase commitment and immediate propagation for global applications. The first protocol ensures replication consistency (with regard to one copy serializability) through the use of a global certification protocol. The second protocol, which is an extension of the first by using propagation locks on primary copies, allows consistency certification to be performed locally for global queries that only read data copies from a single site. We identify and examine the major issues relevant to the proposed protocols.>

Global transaction management requires cooperation from local sites to ensure the consistent and reliable execution of global transactions in a distributed database system. In a heterogeneous distributed database (or multidatabase) environment, various local sites make conflicting assertions of autonomy over the execution of global transactions. A flexible transaction model for the specification of global transactions makes it possible to deal robustly with these conflicting requirements. This paper presents an approach that preserves the semi-atomicity (a weaker form of atomicity) of flexible transactions, allowing local sites to autonomously maintain serializability and recoverability. We offer a fundamental characterization of the flexible transaction model and precisely define the semi-atomicity. We investigate the commit dependencies among the subtransactions of a flexible transaction. These dependencies are used to control the commitment order of the subtransactions. We next identify those restrictions that must be placed upon a flexible transaction to ensure the maintenance of its semi-atomicity. As atomicity is a restrictive criterion, semi-atomicity enhances the class of executable global transactions.

A multidatabase system (MDBS) integrates preexisting and heterogeneous databases in a distributed environment. A multidatabase transaction is a consistent and reliable execution of an application over a multidatabase system. The authors summarize the characteristics of multidatabase transactions and present a multidatabase transaction specification language, the InterBase Parallel Language (IPL). IPL allows users to write MDBS transactions by specifying all associated actions, their sequences, control flow, and data flow among subtransactions, and yet retaining the autonomies of the preexisting software systems. IPL also allows users to specify different commit protocols for different subtransactions and to control the atomicity and isolation granularity of an MDBS transaction. IPL components and design issues are described in detail. The implementation of IPL is also discussed.>

Rapid growth in the area of multidatabase systems (MDBSs), which involve both the access of global data and distributed transaction processing, has created a need for programming languages that provide communication reliability and powerful synchronization. The requirements of MDBSs are reviewed, and the Vienna Parallel Logic programming language is presented. The ways to realize an MDBS communication protocol in this language are discussed. The Vienna Parallel Logic language incorporates a concurrent logic language, as well as features of both distributed operating systems and database management systems. These features combine to support the communication and synchronization required by distributed transaction processing. The Vienna Parallel Logic language is suitable for use as a general-purpose distributed programming and coordination language.>

article Free Access Share on InterBase: a multidatabase prototype systems Authors: O. Bukhres Department of Computer Sciences, Purdue University, West Lafayette, IN Department of Computer Sciences, Purdue University, West Lafayette, INView Profile , J. Chen Department of Computer Sciences, Purdue University, West Lafayette, IN Department of Computer Sciences, Purdue University, West Lafayette, INView Profile , A. Elmagarmid Department of Computer Sciences, Purdue University, West Lafayette, IN Department of Computer Sciences, Purdue University, West Lafayette, INView Profile , X. Liu Department of Computer Sciences, Purdue University, West Lafayette, IN Department of Computer Sciences, Purdue University, West Lafayette, INView Profile , J. Mullen Department of Computer Sciences, Purdue University, West Lafayette, IN Department of Computer Sciences, Purdue University, West Lafayette, INView Profile Authors Info & Claims ACM SIGMOD RecordVolume 22Issue 2June 1, 1993 pp 534–539https://doi.org/10.1145/170036.171545Online:01 June 1993Publication History 2citation264DownloadsMetricsTotal Citations2Total Downloads264Last 12 Months8Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

Article Free Access Share on An InterBase system at BNR Authors: Omran Bukhres BNR Inc., 35 Davis Drive, RTP, NC and Computer Sciences Dept, Purdue University, W. Lafayette, IN BNR Inc., 35 Davis Drive, RTP, NC and Computer Sciences Dept, Purdue University, W. Lafayette, INView Profile , Jiansan Chen BNR Inc., 35 Davis Drive, RTP, NC and Computer Sciences Dept, Purdue University, W. Lafayette, IN BNR Inc., 35 Davis Drive, RTP, NC and Computer Sciences Dept, Purdue University, W. Lafayette, INView Profile , Rob Pezzoli BNR Inc., 35 Davis Drive, RTP, NC BNR Inc., 35 Davis Drive, RTP, NCView Profile Authors Info & Claims SIGMOD '93: Proceedings of the 1993 ACM SIGMOD international conference on Management of dataJune 1993 Pages 426–429https://doi.org/10.1145/170035.170113Online:01 June 1993Publication History 0citation187DownloadsMetricsTotal Citations0Total Downloads187Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

Existing and legacy software systems are the product of lengthy and individual developmental histories. Interoperability among such systems offers the support of global applications on these systems and intelligent information processing. However, interoperability among these heterogeneous systems is hampered by the absence of an integrated environment that would allow the development of global applications requiring intersystem cooperation. A uniform application-system interface is necessary to abstract the common properties of the global applications and of systems, mask their differences, and thus overcome this heterogeneity barrier. This paper presents such a solution, termed Remote System Interfaces (RSIs), which has been designed and implemented in the course of the InterBase project at Purdue University.

A performance evaluation study of two proposed distributed deadlock detection algorithms, the central controller and distributed deadlock detection algorithms, is described. The author examines and reports the magnitude by which these algorithms provide an increase in the throughput, and an increase in the number of blocked, restarted transactions. A performance evaluation model is presented for a distributed database environment. A list of performance parameters and evaluation criteria is included.>

A description is presented of a performance evaluation study of three proposed distributed deadlock detection algorithms, namely, fully centralized, partially distributed, and fully distributed deadlock detection algorithms. The authors investigate and describe the extent to which these algorithms provide an increase in the level of multiprogramming, and an increase in the number of blocked, restarted transactions. A list of performance parameters and evaluation criteria is also described. It is shown that, in general, the partially distributed algorithm provides the best performance.>