DiscoveryLink: A system for integrated access to life sciences data sources

Haas, Laura M.; Schwarz, Peter; Kodali, P.; Kotlar, E.; Rice, Julia E.; Swope, William C.

doi:10.1147/sj.402.0489

Cited by 227 publications

(112 citation statements)

References 23 publications

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“…One major limitation of this approach can be the delays necessary to obtain and process the data. Systems such as TAMBIS [26] and DiscoveryLink [27] use this approach. Recently, due to increased number of systems that provide web-services interfaces to their databases, the use of mediators is being gradually deprecated.…”

Section: Data Integration Modelmentioning

confidence: 99%

GeneBrowser: an approach for integration and functional classification of genomic data

Arrais

Santos

Fernandes

et al. 2007

Journal of Integrative Bioinformatics

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SummaryThe achievements coming from genome analysis depend greatly on the quality of computational and processing methods. Tools for functional mRNA profiling and for gene information integration have become essential to this task. We have developed GeneBrowser as a novel approach that combines the advantages of mRNA profiling tools, at genome-scale experiments, with the features provided by data integration systems. For a given set of genes, GeneBrowser integrates bibliography information with functional annotations, using Gene Ontology, Entrez Gene, KEGG Orthology and KEGG Pathways. The result is a comprehensive and easy to use web application that helps researchers to extract knowledge from large data sets and to speed up the discovery process.

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Section: Data Integration Modelmentioning

confidence: 99%

GeneBrowser: an approach for integration and functional classification of genomic data

Arrais

Santos

Fernandes

et al. 2007

Journal of Integrative Bioinformatics

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“…• Middleware approaches, in which data are combined from multiple sources without creating a physical warehouse, e.g., BioKleisli [10], TAMBIS [1], and DiscoveryLink [16], etc.…”

Section: Related Workmentioning

confidence: 99%

“…DiscoveryLink [16] consists of a federated database engine and a set of wrappers which translate between query fragments and data source API. DiscoveryLink requires the connection to database servers through ODBC, JDBC, OLE, or native DB2 drivers, etc.…”

Section: Related Workmentioning

confidence: 99%

Reconfigurable Web wrapper agents for biological information integration

Hsu

Chang

Hsieh

et al. 2005

J. Am. Soc. Inf. Sci.

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A variety of biological data is transferred and exchanged in overwhelming volumes on the World Wide Web. How to rapidly capture, utilize and integrate the information on the Internet to discover valuable biological knowledge is one of the most critical issues in bioinformatics. Many information integration systems have been proposed for integrating biological data. These systems usually rely on an intermediate software layer called wrappers to access connected information sources. Wrapper construction for Web data sources is often specially hand coded to accommodate the differences between each Web site. However, programming a Web wrapper requires substantial programming skill and is time-consuming and hard to maintain. This paper provides a solution for rapidly building software agents that can serve as Web wrappers for biological information integration. We define an XMLbased language called WNDL, which provides a representation of a Web browsing session. A WNDL script describes how to locate the data, extract the data and combine the data. By executing different WNDL scripts, user can automate virtually all types of Web browsing sessions. We also describe IEPAD, a data extractor based on pattern discovery techniques. IEPAD allows our software agents to automatically discover the extraction rules to extract the contents of a structurally formatted Web page. With a programming-by-example authoring tool, a user can generate a complete Web wrapper agent by browsing the target Web sites. We built a variety of biological applications to demonstrate the feasibility of our approach. The software is available at http://chunnan.iis.sinica.edu.tw/software.html or by contacting the authors.

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“…The most impressive broker is the IBM's DiscoveryLink system (Haas, Schwarz, Kodali, Kotlar.& Swope, 2001). In such system, the language used is SQL and a wrapper is used in order to access database.…”

Section: Introductionmentioning

confidence: 99%