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Bioinformatics Advance Access originally published online on October 31, 2006
Bioinformatics 2007 23(4):524-526; doi:10.1093/bioinformatics/btl523
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

OmicBrowse: a browser of multidimensional omics annotations

Tetsuro Toyoda *, Yoshiki Mochizuki , Keith Player , Naohiko Heida, Norio Kobayashi and Yoshiyuki Sakaki

Genomic Sciences Center, Yokohama Institute RIKEN, 1-77-22, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan

*To whom correspondence should be addressed.


  Abstract

Summary: OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species. OmicBrowse integrates multiple data servers into a single omic space through secure peer-to-peer server communications, so that a user can easily obtain an integrated view of distributed data servers, e.g. an integrated view of numerous whole-genome tiling-array data retrieved from a user's in-house private-data server, along with various genomic annotations from public internet servers. OmicBrowse is especially appropriate for positional-cloning purposes. It displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms. We also show that an omic-space chart effectively represents schemes for integrating multiple datasets of multiple species.

Availability: OmicBrowse is developed by the Genome-Phenome Superbrain Project and is released as free open-source software under the GNU General Public License at http://omicspace.riken.jp

Contact: toyop{at}gsc.riken.go.jp

Associate Editor: Alvis Brazma

Received on May 24, 2006; revised on August 15, 2006; accepted on October 5, 2006

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