DiscoveryLink

Haas, Laura M.; Eckman, Barbara; Kodali, P.; Lin, Eileen; Rice, Julia E.; Schwarz, Peter

doi:10.1016/b978-155860829-0/50013-9

Cited by 8 publications

(8 citation statements)

References 10 publications

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“…We chose IBM's WebSphere Information Integrator (WSII) as the mediator platform (5). Based on the relational data model, WSII makes an autonomous federation of data from heterogeneous sources which appear to the user or front-end application like a single large relational database management system (RDBMS).…”

Section: Features and Functionalitiesmentioning

confidence: 99%

BIPASS: BioInformatics Pipeline Alternative Splicing Services

Lacroix

Legendre

Raschid

et al. 2007

Nucleic Acids Research

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BioInformatics Pipeline Alternative Splicing Services (BIPASS) offer support to scientists interested in gathering information related to alternative splicing (AS) events. The service BIPAS–SpliceDB provides access to AS information that has been extracted a priori from various public databases and stored in a data warehouse. In contrast, the BIPAS–Align&Splice service allows scientists to submit their own sequences and genome to compute AS analysis results. BIPAS services offer various user-friendly ways to navigate through the results. AS results are organized at different conceptual levels (clusters and sequences), and are displayed in graphs or summarized in tables that can be downloaded in XML or text format. The two BIPAS services SpliceDB and Align&Splice are available online at http://bip.umiacs.umd.edu:8080/.

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Section: Features and Functionalitiesmentioning

confidence: 99%

BIPASS: BioInformatics Pipeline Alternative Splicing Services

Lacroix

Legendre

Raschid

et al. 2007

Nucleic Acids Research

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“…DiscoveryLink 42,43,45 is the extension for life sciences of DataJoiner and DB2 15 merged with Garlic. 21 DiscoveryLink and the underlying Garlic mediator integrates relational, flat file and Web resources and encapsulates the access to specialized search capabilities into user-defined functions.…”

Section: Existing Biomolecular Database Systemsmentioning

confidence: 99%

“…They include BioKleisli 11,26 and its extensions K2 25,73 and Pizzkell/Kleisli, 19,87 the TINet multidatabase system based on the Object Protocol Model (OPM) and its 28,50 DiscoveryLink,42,43,45 an extension for life sciences of DataJoiner and DB2 15 merged with Garlic, 21 P/FDM 47-49 and TAMBIS. 3,72 These systems, that will be discussed in detail in Sec.…”

mentioning

confidence: 99%

Techniques for Optimization of Queries on Integrated Biological Resources

Lacroix

Raschid

Eckman

2004

J. Bioinform. Comput. Biol.

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Today, scientific data are inevitably digitized, stored in a wide variety of formats, and are accessible over the Internet. Scientific discovery increasingly involves accessing multiple heterogeneous data sources, integrating the results of complex queries, and applying further analysis and visualization applications in order to collect datasets of interest. Building a scientific integration platform to support these critical tasks requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that are locally materialized in warehouses or generated by software. The lack of efficiency of existing approaches can significantly affect the process with lengthy delays while accessing critical resources or with the failure of the system to report any results. Some queries take so much time to be answered that their results are returned via email, making their integration with other results a tedious task. This paper presents several issues that need to be addressed to provide seamless and efficient integration of biomolecular data. Identified challenges include: capturing and representing various domain specific computational capabilities supported by a source including sequence or text search engines and traditional query processing; developing a methodology to acquire and represent semantic knowledge and metadata about source contents, overlap in source contents, and access costs; developing cost and semantics based decision support tools to select sources and capabilities, and to generate efficient query evaluation plans.

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“…For example, a scientist expecting to obtain the best (more complete) characterization of a gene may choose a path that maximizes the number of attributes. BioNavigation will be coupled with the DiscoveryLink mediation system [3] to execute the queries when the evaluation path has been selected.…”

Section: Discussionmentioning

confidence: 99%

“…It takes time to interrogate a new data source; to understand and become familiar with its format, capabilities, and the quality of the data it provides. Yet most systems currently available to scientists that provide access to integrated biological resources, including DiscoveryLink [3], TAMBIS [4], and SRS [5], expect the user to specify explicitly the resources involved in the data collection process, or the system transparently chooses a particular database for the user. Both approaches raise critical issues and may affect the data collection process, and thus the quality and completeness of the retrieved data.…”

Section: Introductionmentioning

confidence: 99%

Exploiting multiple paths to express scientific queries

Lacroix¹,

Morris²,

Parekh³

et al.

Proceedings. 16th International Conference on Scientific and Statistical Database Management, 2004.

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The purpose of this demonstration is to present the main features of the BioNavigation system. Scientific data collection needed in various stages of scientific discovery is typically performed manually. For each scientific object of interest (e.g., a gene, a sequence), scientists query a succession of Web resources following links between retrieved entries. Each of the steps provides part of the intended characterization of the scientific object. This process is sometimes partially supported by hard-coded scripts or complex queries that will be evaluated by a mediation-based data integration system or against a data warehouse. These approaches fail in guiding the scientists during the collection process. In contrast, the BioNavigation approach presented in the paper provides the scientists with information on the available alternative resources, their provenance, and the costs of data collection. The BioNavigation system enhances a mediation-based integration system and provides scientists with support for the following:To ask queries at a high conceptual level; To visualize the multiple alternative resources that may be exploited to execute their data collection queries; To choose the final execution path to evaluate their queries.

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DiscoveryLink

Cited by 8 publications

References 10 publications

BIPASS: BioInformatics Pipeline Alternative Splicing Services

BIPASS: BioInformatics Pipeline Alternative Splicing Services

Techniques for Optimization of Queries on Integrated Biological Resources

Exploiting multiple paths to express scientific queries

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