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Mamm Genome. 2012 Oct;23(9-10):550-8. doi: 10.1007/s00335-012-9408-0. Epub 2012 Jul 31.

BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration.

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1
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA. ringwald@informatics.jax.org

Abstract

Mouse gene expression data are complex and voluminous. To maximize the utility of these data, they must be made readily accessible through databases, and those resources need to place the expression data in the larger biological context. Here we describe two community resources that approach these problems in different but complementary ways: BioGPS and the Mouse Gene Expression Database (GXD). BioGPS connects its large and homogeneous microarray gene expression reference data sets via plugins with a heterogeneous collection of external gene centric resources, thus casting a wide but loose net. GXD acquires different types of expression data from many sources and integrates these data tightly with other types of data in the Mouse Genome Informatics (MGI) resource, with a strong emphasis on consistency checks and manual curation. We describe and contrast the "loose" and "tight" data integration strategies employed by BioGPS and GXD, respectively, and discuss the challenges and benefits of data integration. BioGPS is freely available at http://biogps.org . GXD is freely available through the MGI web site ( www.informatics.jax.org ) or directly at www.informatics.jax.org/expression.shtml .

PMID:
22847375
PMCID:
PMC3469763
DOI:
10.1007/s00335-012-9408-0
[Indexed for MEDLINE]
Free PMC Article
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