Abstract
In this article, we describe the use of the BioMart data management system to provide integrated access to International Knockout Mouse Consortium (IKMC) data and other related mouse resources. The IKMC is currently mutating all mouse protein-coding genes in embryonic stem (ES) cells using gene targeting and gene trapping approaches. The BioMart portal allows researchers to identify and obtain IKMC knockout vectors, ES cells and mice for genes of interest. Gene annotation, expression, phenotype and disease data is also integrated from external BioMarts, allowing selection of IKMC products by a wide variety of criteria. These products are invaluable for researchers involved in the elucidation of gene function and the role of individual genes in human disease. Here, we describe these datasets in more detail and illustrate the functionality of the portal using several examples.Database URL: http://www.knockoutmouse.org/mart
Highlights
The International Knockout Mouse Consortium (IKMC) consists of KOMP [KnockOut Mouse Project; [2]] funded by the National Institutes of Health (NIH, USA); EUCOMM [(3); EUropean Conditional Mouse Mutagenesis Program] funded by the European Commission (EC), NorCOMM (North American Conditional Mouse Mutagenesis Project) funded by Genome Canada and the Texas Institute of Genomic Medicine [TIGM; [4]]
We have demonstrated how BioMart is a useful way of exposing the data being generated by the IKMC
It allows researchers to query on a wide range of criteria and identify physical resources such as vectors, embryonic stem (ES) cells and mouse lines to order from the repositories associated with the IKMC
Summary
BioMart as an integration solution for the International Knockout Mouse Consortium. In this article, we describe the use of the BioMart data management system to provide integrated access to International Knockout Mouse Consortium (IKMC) data and other related mouse resources. The BioMart portal allows researchers to identify and obtain IKMC knockout vectors, ES cells and mice for genes of interest. Expression, phenotype and disease data is integrated from external BioMarts, allowing selection of IKMC products by a wide variety of criteria. These products are invaluable for researchers involved in the elucidation of gene function and the role of individual genes in human disease. We describe these datasets in more detail and illustrate the functionality of the portal using several examples.
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