BioGPS


Microarrays, next-generation sequencing, and genomic screening technologies have enabled researchers to perform experiments on genome-wide scale. These highly-parallel technologies allow researchers to quickly generate candidate gene lists. However, prioritizing those gene lists for follow up testing is still a manual process. This challenge is particularly daunting when gene lists are often dominated by genes which are unfamiliar to any single researcher.

BioGPS is a gene annotation portal that emphasizes user customizability and community extensibility.
Many online tools attempt to summarize current knowledge of each gene. For example, gene portals like Entrez Gene and Ensembl present key information on genomic location and context, Gene Ontology terms, mRNA and protein sequences, and common synonyms and aliases. However, they don’t contain information on knockout phenotypes in model organisms, information presented through sites like the Mouse Genome Database and Rat Genome Database. Still other sites such as KEGG, Reactome, and WikiPathways present information on a gene’s pathway context. The number of sites that provide gene-centric data easily numbers in the hundreds.

This fragmented landscape of gene annotation resources is clearly cumbersome for end users. Visiting multiple sites for every gene is time-consuming and laborious. Moreover, continuously staying abreast of all the relevant resources is an impossible task. This fragmented state of gene annotation is also cumbersome for developers of bioinformatics tools. Each site spends significant effort duplicating data and features of existing sites instead of focusing on their new and novel content.

To address these inefficiencies, we created a new gene annotation portal called BioGPS, which emphasizes two key design principles: user customizability and community extensibility. The focus on user customizability ensures that each user can easily access all the gene annotation resources that are most relevant to them, whether they are a molecular biologist, a geneticist, or a systems biologist. The emphasis on community extensibility enables developers to easily integrate their novel data within the BioGPS platform.

BioGPS receives millions of hits per year, and is freely and publicly available at biogps.org.

 

References

Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, 3rd and Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol, 10:R130. (PubMed) (PDF)

Ringwald M, Wu C, Su AI (2012) BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. Mamm Genome. 23(9-10):550-8. (Pubmed) (PDF)

Wu C, Macleod I, Su AI. (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res. 41(D1):D561-5. doi: 10.1093/nar/gks1114. (PubMed) (PDF)