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Extending traditional query-based integration approaches for functional characterization of post-genomic data

Eckman, Barbara A. ; Kosky, Anthony S. ; Laroco, Jr, Leonardo A.

Bioinformatics, 2001-07, Vol.17 (7), p.587-601 [Revista revisada por pares]

Oxford: Oxford University Press

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Título:
Extending traditional query-based integration approaches for functional characterization of post-genomic data
Autor: Eckman, Barbara A. ; Kosky, Anthony S. ; Laroco, Jr, Leonardo A.
Materias: Animals ; Biological and medical sciences ; Computational Biology ; Database Management Systems ; Databases as Topic ; DNA, Complementary - genetics ; Fundamental and applied biological sciences. Psychology ; Gene Expression ; General aspects ; Genome ; Genome, Human ; Humans ; Internet ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Mice ; Phosphotransferases - genetics ; Software
Es parte de: Bioinformatics, 2001-07, Vol.17 (7), p.587-601
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Descripción: Motivation: To identify and characterize regions of functional interest in genomic sequence requires full, flexible query access to an integrated, up-to-date view of all related information, irrespective of where it is stored (within an organization or across the Internet) and its format (traditional database, flat file, web site, results of runtime analysis). Wide-ranging multi-source queries often return unmanageably large result sets, requiring non-traditional approaches to exclude extraneous data. Results: Target Informatics Net (TINet) is a readily extensible data integration system developed at GlaxoSmith- Kline (GSK), based on the Object-Protocol Model (OPM) multidatabase middleware system of Gene Logic Inc. Data sources currently integrated include: the Mouse Genome Database (MGD) and Gene Expression Database (GXD), GenBank, SwissProt, PubMed, GeneCards, the results of runtime BLAST and PROSITE searches, and GSK proprietary relational databases. Special-purpose class methods used to filter and augment query results include regular expression pattern-matching over BLAST HSP alignments and retrieving partial sequences derived from primary structure annotations. All data sources and methods are accessible through an SQL-like query language or a GUI, so that when new investigations arise no additional programming beyond query specification is required. The power and flexibility of this approach are illustrated in such integrated queries as: (1) ‘find homologs in genomic sequence to all novel genes cloned and reported in the scientific literature within the past three months that are linked to the MeSH term ‘neoplasms”; (2) ‘using a neuropeptide precursor query sequence, return only HSPs where the target genomic sequences conserve the G[KR][KR] motif at the appropriate points in the HSP alignment’; and (3) ‘of the human genomic sequences annotated with exon boundaries in GenBank, return only those with valid putative donor/acceptor sites and start/stop codons’. Availability: Freely available to non-profit educational and research institutions. Usage by commercial entities requires a license agreement. Contact: barbara_eckman@sbphrd.com * To whom correspondence should be addressed.
Editor: Oxford: Oxford University Press
Idioma: Inglés

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Extending traditional query-based integration approaches for functional characterization of post-genomic data

Eckman, Barbara A. ; Kosky, Anthony S. ; Laroco, Jr, Leonardo A.

Oxford: Oxford University Press

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