InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

被引：173

作者：

Smith, Richard N. ^{[1
,2
]}

Aleksic, Jelena ^{[1
,2
]}

Butano, Daniela ^{[1
,2
]}

Carr, Adrian ^{[1
,2
]}

Contrino, Sergio ^{[1
,2
]}

Hu, Fengyuan ^{[1
,2
]}

Lyne, Mike ^{[1
,2
]}

Lyne, Rachel ^{[1
,2
]}

Kalderimis, Alex ^{[1
,2
]}

Rutherford, Kim ^{[1
,2
]}

Stepan, Radek ^{[1
,2
]}

Sullivan, Julie ^{[1
,2
]}

Wakeling, Matthew ^{[1
,2
]}

Watkins, Xavier ^{[1
,2
]}

Micklem, Gos ^{[1
,2
]}

机构：

[1] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

[2] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge CB2 1QR, England

来源：

BIOINFORMATICS | 2012年 / 28卷 / 23期

基金：

英国惠康基金;

关键词：

D O I：

10.1093/bioinformatics/bts577

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.

引用

页码：3163 / 3165

页数：3

共 11 条

[1] YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit [J].

Balakrishnan, Rama ;

Park, Julie ;

Karra, Kalpana ;

Hitz, Benjamin C. ;

Binkley, Gail ;

Hong, Eurie L. ;

Sullivan, Julie ;

Micklem, Gos ;

Cherry, J. Michael .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,

[2] Unlocking the secrets of the genome [J].

Celniker, Susan E. ;

Dillon, Laura A. L. ;

Gerstein, Mark B. ;

Gunsalus, Kristin C. ;

Henikoff, Steven ;

Karpen, Gary H. ;

Kellis, Manolis ;

Lai, Eric C. ;

Lieb, Jason D. ;

MacAlpine, David M. ;

Micklem, Gos ;

Piano, Fabio ;

Snyder, Michael ;

Stein, Lincoln ;

White, Kevin P. ;

Waterston, Robert H. .

NATURE, 2009, 459 (7249) :927-930

[3]

Chen, 2011, PLOS ONE, V6

[4] modMine: flexible access to modENCODE data [J].

Contrino, Sergio ;

Smith, Richard N. ;

Butano, Daniela ;

Carr, Adrian ;

Hu, Fengyuan ;

Lyne, Rachel ;

Rutherford, Kim ;

Kalderimis, Alex ;

Sullivan, Julie ;

Carbon, Seth ;

Kephart, Ellen T. ;

Lloyd, Paul ;

Stinson, E. O. ;

Washington, Nicole L. ;

Perry, Marc D. ;

Ruzanov, Peter ;

Zha, Zheng ;

Lewis, Suzanna E. ;

Stein, Lincoln D. ;

Micklem, Gos .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D1082-D1088

[5] The Sequence Ontology: a tool for the unification of genome annotations [J].

Eilbeck, K ;

Lewis, SE ;

Mungall, CJ ;

Yandell, M ;

Stein, L ;

Durbin, R ;

Ashburner, M .

GENOME BIOLOGY, 2005, 6 (05)

[6] Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences [J].

Goecks, Jeremy ;

Nekrutenko, Anton ;

Taylor, James .

GENOME BIOLOGY, 2010, 11 (08)

[7] FlyMine:: an integrated database for Drosophila and Anopheles genomics [J].

Lyne, Rachel ;

Smith, Richard ;

Rutherford, Kim ;

Wakeling, Matthew ;

Varley, Andrew ;

Guillier, Francois ;

Janssens, Hilde ;

Ji, Wenyan ;

Mclaren, Peter ;

North, Philip ;

Rana, Debashis ;

Riley, Tom ;

Sullivan, Julie ;

Watkins, Xavier ;

Woodbridge, Mark ;

Lilley, Kathryn ;

Russell, Steve ;

Ashburner, Michael ;

Mizuguchi, Kenji ;

Micklem, Gos .

GENOME BIOLOGY, 2007, 8 (07)

[8] FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database [J].

Pfreundt, Ulrike ;

James, Daniel P. ;

Tweedie, Susan ;

Wilson, Derek ;

Teichmann, Sarah A. ;

Adryan, Boris .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D443-D447

[9]

Shimoyama Mary, 2011, Human Genomics, V5, P124

[10] MitoMiner: a data warehouse for mitochondrial proteomics data [J].

Smith, Anthony C. ;

Blackshaw, James A. ;

Robinson, Alan J. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D1160-D1167

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