Biological workflow with BlastQuest

William G. Farmerie, Joachim Hammer, Li Liu, Anuj Sahni, Markus Schneider

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Besides domain-specific biological problems, biologists are confronted with many computational problems. The large amount of varying, heterogeneous, and semi-structured biological data, the increasing complexity of biological applications, methods, and tools afflicted with uncertainty and missing knowledge, as well as the lacking interoperability of available tools necessitate integrative measures to enable biology workflow. In this paper we address these problems in the context of the processing and evaluation of BLAST query results. We present a new tool, called BlastQuest, which relies on database technology and provides sophisticated interactive and Web-enabled query, analysis, and visualization facilities for genomics data. The interface with the Gene Ontology and the KEGG pathway databases decisively foster the biological workflow. Finally, based on our experience with BlastQuest, we briefly sketch a new concept, called Genomics Algebra, for solving genomic data management problems from a broader perspective.

Original languageEnglish (US)
Pages (from-to)75-97
Number of pages23
JournalData and Knowledge Engineering
Volume53
Issue number1
DOIs
StatePublished - Apr 2005
Externally publishedYes

Fingerprint

Interoperability
Information management
Algebra
Interfaces (computer)
Ontology
Visualization
Genes
Processing
Genomics
Data base
Query
Uncertainty
Data management
Evaluation
Pathway
World Wide Web
Gene

Keywords

  • BLAST
  • Gene Ontology
  • Genomics Algebra
  • KEGG pathway database
  • Unifying database

ASJC Scopus subject areas

  • Artificial Intelligence

Cite this

Farmerie, W. G., Hammer, J., Liu, L., Sahni, A., & Schneider, M. (2005). Biological workflow with BlastQuest. Data and Knowledge Engineering, 53(1), 75-97. https://doi.org/10.1016/j.datak.2004.06.014

Biological workflow with BlastQuest. / Farmerie, William G.; Hammer, Joachim; Liu, Li; Sahni, Anuj; Schneider, Markus.

In: Data and Knowledge Engineering, Vol. 53, No. 1, 04.2005, p. 75-97.

Research output: Contribution to journalArticle

Farmerie, WG, Hammer, J, Liu, L, Sahni, A & Schneider, M 2005, 'Biological workflow with BlastQuest', Data and Knowledge Engineering, vol. 53, no. 1, pp. 75-97. https://doi.org/10.1016/j.datak.2004.06.014
Farmerie, William G. ; Hammer, Joachim ; Liu, Li ; Sahni, Anuj ; Schneider, Markus. / Biological workflow with BlastQuest. In: Data and Knowledge Engineering. 2005 ; Vol. 53, No. 1. pp. 75-97.
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