TY - JOUR
T1 - BioExtract server-An integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data
AU - Lushbough, Carol
AU - Bergman, Michael K.
AU - Lawrence, Carolyn J.
AU - Jennewein, Doug
AU - Brendel, Volker
N1 - Funding Information:
The development of the FSDW System was originally funded by the National Human Genome Research Institute Grant 2R44HG001850-03 to Michael Bergman, VisualMetrics Corp. The BioExtract Server project was supported in part by the US National Science Foundation Grants DBI-0090732, DBI-0321600, and DBI-0606909 to Volker Brendel. The authors would like to thank the anonymous reviewers and the editor Dr. Ludaescher for many helpful comments on earlier versions of their manuscript.
PY - 2010/1
Y1 - 2010/1
N2 - Many in silico investigations in bioinformatics require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community databases, and project databases for use in domain-specific research. Different data sources frequently utilize distinct query languages and return results in unique formats, and therefore researchers must either rely upon a small number of primary data sources or become familiar with multiple query languages and formats. Similarly, the associated analytic tools often require specific input formats and produce unique outputs which make it difficult to utilize the output from one tool as input to another. The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to consolidate, analyze, and serve data from heterogeneous biomolecular databases in the form of a mash-up. The basic operations of the BioExtract Server allow researchers, via their Web browsers, to specify data sources, flexibly query data sources, apply analytic tools, download result sets, and store query results for later reuse. As a researcher works with the system, their steps are saved in the background. At any time, these steps can be preserved long-term as a workflow simply by providing a workflow name and description.
AB - Many in silico investigations in bioinformatics require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community databases, and project databases for use in domain-specific research. Different data sources frequently utilize distinct query languages and return results in unique formats, and therefore researchers must either rely upon a small number of primary data sources or become familiar with multiple query languages and formats. Similarly, the associated analytic tools often require specific input formats and produce unique outputs which make it difficult to utilize the output from one tool as input to another. The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to consolidate, analyze, and serve data from heterogeneous biomolecular databases in the form of a mash-up. The basic operations of the BioExtract Server allow researchers, via their Web browsers, to specify data sources, flexibly query data sources, apply analytic tools, download result sets, and store query results for later reuse. As a researcher works with the system, their steps are saved in the background. At any time, these steps can be preserved long-term as a workflow simply by providing a workflow name and description.
KW - Bioinformatics (genome or protein) databases
KW - Data integration
KW - Database integration
KW - Distributed architectures
KW - Heterogeneous Databases.
KW - Heterogeneous databases
KW - Mash-up
KW - Scientific workflow automation.
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U2 - 10.1109/TCBB.2008.98
DO - 10.1109/TCBB.2008.98
M3 - Article
C2 - 20150665
AN - SCOPUS:76849094662
SN - 1545-5963
VL - 7
SP - 12
EP - 24
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics
IS - 1
M1 - 4626945
ER -