Genome Biol. 2009;10(11):R130. Epub 2009 Nov 17.

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI.

Source

Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA. cwu@gnf.org

Abstract

Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS http://biogps.gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.

PMID:: 19919682; [PubMed - indexed for MEDLINE]
PMCID: PMC3091323

Free PMC Article

Images from this publication.See all images (3) Free text

Publication Types, MeSH Terms, Grant Support

Publication Types

MeSH Terms

Grant Support

GM083924/GM/NIGMS NIH HHS/United States

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Libraries

LinkOut Holdings

Supplemental Content

Related citations

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. [BMC Bioinformatics. 2007]
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.
Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA. BMC Bioinformatics. 2007 Nov 2; 8:426. Epub 2007 Nov 2.
The Gene Wiki: community intelligence applied to human gene annotation. [Nucleic Acids Res. 2010]
The Gene Wiki: community intelligence applied to human gene annotation.
Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI. Nucleic Acids Res. 2010 Jan; 38(Database issue):D633-9. Epub 2009 Sep 15.
GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. [BMC Bioinformatics. 2005]
GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.
Kirov SA, Peng X, Baker E, Schmoyer D, Zhang B, Snoddy J. BMC Bioinformatics. 2005 Mar 24; 6:72. Epub 2005 Mar 24.
Review FlyBase : a database for the Drosophila research community. [Methods Mol Biol. 2008]
Review FlyBase : a database for the Drosophila research community.
Drysdale R, FlyBase Consortium. Methods Mol Biol. 2008; 420:45-59.
Review Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. [Front Biosci. 2007]
Review Integration of bioinformatics resources for functional analysis of gene expression and proteomic data.
Huang H, Hu ZZ, Arighi CN, Wu CH. Front Biosci. 2007 Sep 1; 12:5071-88. Epub 2007 Sep 1.

See reviews... See all...

Cited by 54 PubMed Central articles

5-alpha-reductase type I (SRD5A1) is up-regulated in non-small cell lung cancer but does not impact proliferation, cell cycle distribution or apoptosis. [Cancer Cell Int. 2012]
5-alpha-reductase type I (SRD5A1) is up-regulated in non-small cell lung cancer but does not impact proliferation, cell cycle distribution or apoptosis.
Kapp FG, Sommer A, Kiefer T, Dölken G, Haendler B. Cancer Cell Int. 2012 Jan 18; 12(1):1. Epub 2012 Jan 18.
Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity. [Transcription. 2011]
Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity.
Koch F, Andrau JC. Transcription. 2011 Nov; 2(6):263-8. Epub 2011 Nov 1.
Identifying single copy orthologs in Metazoa. [PLoS Comput Biol. 2011]
Identifying single copy orthologs in Metazoa.
Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. PLoS Comput Biol. 2011 Dec; 7(12):e1002269. Epub 2011 Dec 1.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

BioGPS: an extensible and customizable portal for querying and organizing gene a...
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
Genome Biol. 2009 ;10(11):R130. Epub 2009 Nov 17 .

PubMed
On the association between chromosomal rearrangements and genic evolution in hum...
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.
Genome Biol. 2007 ;8(10):R230.

PubMed
Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution a...
Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.
Genome Biol. 2002 Aug 29 ;3(9):research0051. Epub 2002 Aug 29 .

PubMed
The hidden universal distribution of amino acid biosynthetic networks: a genomic...
The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution.
Genome Biol. 2008 ;9(6):R95. Epub 2008 Jun 9 .

PubMed
Use of high-density tiling microarrays to identify mutations globally and elucid...
Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum.
Genome Biol. 2009 Feb 13 ;10(2):R21.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: