Using BioMart as a framework to manage and query pancreatic cancer data.

Abstract

We describe the Pancreatic Expression Database (PED), the first cancer database originally designed based on the BioMart infrastructure. The PED portal brings together multidimensional pancreatic cancer data from the literature including genomic, proteomic, miRNA and gene expression profiles. Based on the BioMart 0.7 framework, the database is easily integrated with other BioMart-compliant resources, such as Ensembl and Reactome, to give access to a wide range of annotations alongside detailed experimental conditions. This article is intended to give an overview of PED, describe its data content and work through examples of how to successfully mine and integrate pancreatic cancer data sets and other BioMart resources.

• Authors: Rosalind J Cutts, Emanuela Gadaleta, Nicholas R Lemoine, Claude Chelala
• Journal: Database : the journal of biological databases and curation (Database (Oxford)) Vol. 2011 Pg. bar024 ( 2011) ISSN: 1758-0463 [Electronic] England
• PMID: 21666272 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• MicroRNAs

Topics

• Computational Biology (methods)
• DNA Copy Number Variations (genetics)
• Database Management Systems
• Databases, Genetic
• Gene Expression Regulation, Neoplastic
• Humans
• Internet
• MicroRNAs (genetics)
• Pancreatic Neoplasms (genetics)
• Search Engine
• Software