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SNPit: a federated data integration system for the purpose of functional SNP annotation.


ABSTRACT: Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was included through an inference engine plug in. The SNPit web servlet is available online for use. SNPit allows users to go to one source for up-to-date information on the functional annotation of SNPs. A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies.

SUBMITTER: Shen TH 

PROVIDER: S-EPMC2680224 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature

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SNPit: a federated data integration system for the purpose of functional SNP annotation.

Shen Terry H TH   Carlson Christopher S CS   Tarczy-Hornoch Peter P  

Computer methods and programs in biomedicine 20090326 2


Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNP  ...[more]

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