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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #285216

Title: GrameneMart: the biomart data portal for the gramene project

item SPOONER, WILLIAM - Cold Spring Harbor Laboratory
item YOUENS-CLARK, KEN - Cold Spring Harbor Laboratory
item STAINES, DANIEL - European Bioinformatics Institute
item Ware, Doreen

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2011
Publication Date: 2/28/2012
Citation: Spooner, W., Youens-Clark, K., Staines, D., Ware, D. 2012. GrameneMart: the biomart data portal for the gramene project. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar056.

Interpretive Summary: BioMart is a tool designed to allow biologists to easily create complex queries of very large datasets and retrieve the results in a variety of common and useful formats. The Gramene database began using BioMart early on and has benefited from using this powerful and ubiquitous tool. Gramene Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps, and provides an integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The Gramene BioMart instance provides an easy-to-use interface, and robust programmatic access, to support integration of Gramene data with other resources. In this paper, we describe the data that can be extracted from Gramene’s BioMart instance.

Technical Abstract: The Gramene project was an early adopter of the BioMart software, which remains an integral and well-used component of the Gramene web site. BioMart accessible data sets include plant gene annotations, plant variation catalogues, genetic markers, physical mapping entities, public DNA/mRNA sequences of various types and curated QTL for various species.