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Titolo:
MetaFam: a unified classification of protein families. II. Schema and query capabilities
Autore:
Shoop, E; Silverstein, KAT; Johnson, JE; Retzel, EF;
Indirizzi:
Univ Minnesota, Acad Hlth Ctr, Comp Biol Ctr, Minneapolis, MN 55455 USA Univ Minnesota Minneapolis MN USA 55455 ol Ctr, Minneapolis, MN 55455 USA
Titolo Testata:
BIOINFORMATICS
fascicolo: 3, volume: 17, anno: 2001,
pagine: 262 - 271
SICI:
1367-4803(200103)17:3<262:MAUCOP>2.0.ZU;2-Z
Fonte:
ISI
Lingua:
ENG
Soggetto:
SEQUENCE DATABASE CLASSIFICATION; RETRIEVAL-SYSTEM; BIOLOGY; INTEGRATION; ALIGNMENTS; SEARCH; ENTREZ; FOLDS; PIR; SET;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
44
Recensione:
Indirizzi per estratti:
Indirizzo: Shoop, E Univ Minnesota, Acad Hlth Ctr, Comp Biol Ctr, Mayo Mail Code 420 Delaware St SE, Minneapolis, MN 55455 USA Univ Minnesota Mayo Mail Code 420Delaware St SE Minneapolis MN USA 55455
Citazione:
E. Shoop et al., "MetaFam: a unified classification of protein families. II. Schema and query capabilities", BIOINFORMAT, 17(3), 2001, pp. 262-271

Abstract

Motivation: Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required toaid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data, This paper presents the global schema, integration issues, and query capabilities of MetaFam. Results: MetaFam is an integrated data warehouse of information about protein families and their sequences. This data has been collected into a consistent global schema, and stored in an Oracle relational database. The warehouse implementation allows for quick removal of outdated data sets, in addition to the relational implementation of the primary schema, we have developed several derived tables that enable efficient access from data visualization and exploration tools. Through a series of straightforward SQL queries, we demonstrate the usefulness of this data warehouse for comparing protein family classifications and for functional assignment of new sequences. Availability: Access to the MetaFam database is provided through a Java applet called MetaFamView, which can be run from the MetaFam web site at http://www.metafam. ahc.umn.edu/. Access to the relational data via named Oracle accounts can be arranged with the authors. Arrangements can also be made to obtain the data in Oracle 'export dump' format. Supplementary information: The complete relational schema, integration scripts, and analysis queries are available from the authors.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 03/04/20 alle ore 10:38:03