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TabSQL: a MySQL tool to facilitate mapping user data to public databases

Xiao-Qin Xia1, Michael McClelland12 and Yipeng Wang12

Author Affiliations

1 Vaccine Research Institute of San Diego, 10835 Road to the Cure, San Diego, CA 92121, USA

2 Department of Pathology & Laboratory Medicine, University of California, Irvine, CA 92697, USA

BMC Bioinformatics 2010, 11:342  doi:10.1186/1471-2105-11-342

Published: 23 June 2010



With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases.


We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line.


TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.