Free online tool by STSI researchers allows users to access a wide array of gene annotation resources
Advances in next-generation sequencing and genomic screening technologies have led to an explosion in the amount of biomedical information that is currently available to researchers. Candidate gene lists can be generated faster than ever before and the portfolio of available online resources that provide gene-centric data is rapidly increasing, becoming more and more specialized in the process. This rapid growth in data has led to a fragmented landscape of gene annotation resources that can be challenging and laborious for researchers and developers to navigate, who may have to consult multiple websites to obtain the information that they need.
In 2008, Dr. Andrew Su, Associate Professor in the Department of Molecular and Experimental Medicine at the Scripps Research Institute (TSRI) and a faculty member at the Scripps Translational Science Institute (STSI), decided to tackle this issue by launching a centralized gene-annotation portal that allows users to access multiple gene-specific annotation resources through a browser-based plugin interface. Dr. Su sought to create a tool to clearly visualize and easily share large datasets, and to pool together disparate resources to help analyze them. The platform, called BioGPS, was designed with two guiding principles in mind – customizability and extensibility. Users are able to control which data are displayed in the customizable layout, and can add new plugins to the portal to extend its capabilities.
“Allowing users to easily create and share plugins enables them to integrate information from various resources,” explained Dr. Chunlei Wu, Associate Professor of Molecular Medicine at TSRI and the primary developer behind BioGPS. “This sets BioGPS apart from many other web-based gene-centric annotation portals.”
By enabling users to independently contribute new resources, BioGPS seeks to build a user community that helps ensure that researchers and developers are able to access up-to-date gene annotation resources that are most relevant to them through a free, open resource. Also importantly, users are not dependent on portal administrators for new content.
According to Ginger Tsueng, Scientific Outreach Project Manager in the Su Lab, “BioGPS is extremely versatile, and not geared towards one particular type of researcher. Whether you’re a cell biologist, geneticist, immunologist or any other kind of researcher, BioGPS allows you to customize your own portal in a unified interface and add new resources as needed.”
Since its initial launch, the user-base of BioGPS has been steadily growing. Currently the portal receives over 132,000 page views from approximately 14,500 unique users each month. Users, who have access to over 640 plugins and around 6000 datasets, are performing over 50,000 gene searches each month on average.
Dr. Su and his team recently published an article in Nucleic Acids Research Advance Access in which they provide an update on the latest additions to BioGPS and give a detailed overview of the functionality of the tool.
To learn more, read the article in Nucleic Acids Research, or visit BioGPS.org.
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