OmicBrowse: a Flash-based high-performance graphics interface for genomic resources

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Abstract

OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. It is an open source tool capable of regulating multiple user data access to each dataset to allow multiple users to have their own integrative view of both their unpublished and published datasets, so that the maintenance costs related to supplying each collaborator exclusively with their own private data are significantly reduced. OmicBrowse supports DAS1 imports and exports of annotations to Internet site servers worldwide. We also provide a data-download named OmicDownload server that interactively selects datasets and filters the data on the selected datasets. Our OmicBrowse server has been freely available at http://omicspace.riken.jp/ since its launch in 2003. The OmicBrowse source code is downloadable from http://sourceforge.net/projects/omicbrowse/.

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Most cited references 20

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The generic genome browser: a building block for a model organism system database.

Lincoln D. Stein, Christopher John Mungall, ShengQiang Shu … (2002)

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.

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Entrez Gene: gene-centered information at NCBI

Donna R. Maglott, Jim Ostell, Kim D. Pruitt … (2004)

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.

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The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Seung Rhee, William D. Beavis, Tanya Berardini … (2003)

Arabidopsis thaliana is the most widely-studied plant today. The concerted efforts of over 11 000 researchers and 4000 organizations around the world are generating a rich diversity and quantity of information and materials. This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers and can be searched and downloaded in a number of ways. In the last two years, efforts have been focused on increasing data content and diversity, functionally annotating genes and gene products with controlled vocabularies, and improving data retrieval, analysis and visualization tools. New information include sequence polymorphisms including alleles, germplasms and phenotypes, Gene Ontology annotations, gene families, protein information, metabolic pathways, gene expression data from microarray experiments and seed and DNA stocks. New data visualization and analysis tools include SeqViewer, which interactively displays the genome from the whole chromosome down to 10 kb of nucleotide sequence and AraCyc, a metabolic pathway database and map tool that allows overlaying expression data onto the pathway diagrams. Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system.

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Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 1 July 2009

Publication date (Print): 1 July 2009

Publication date (Electronic): 15 June 2009

Publication date PMC-release: 15 June 2009

Volume: 37

Issue: Web Server issue

Pages: W57-W62

Affiliations

Bioinformatics and Systems Engineering division (BASE), RIKEN (The Institute of Physical and Chemical Research), 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan

Author notes

*To whom correspondence should be addressed. Tel: +81-45-503-9610; Fax: +81-45-503-9553; Email: toyoda@ 123456base.riken.jp

Article

Publisher ID: gkp404

DOI: 10.1093/nar/gkp404

PMC ID: 2703975

PubMed ID: 19528066

SO-VID: ed597c27-9eb3-4a2e-83ac-62e058905be5

License:

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.

History

Date received : 31 January 2009

Date revision received : 18 April 2009

Date accepted : 2 May 2009

OmicBrowse: a Flash-based high-performance graphics interface for genomic resources

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Abstract

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Genomic Prediction

Most cited references 20

The generic genome browser: a building block for a model organism system database.

Entrez Gene: gene-centered information at NCBI

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

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