Researchers from the Genomics Institute of the Novartis Research Foundation have published a paper describing a new resource for organizing and querying gene annotations. Called BioGPS, the new information portal is based on a compilation of existing genetic resources.
The portal, which is accessible for free online, allows researchers to search through many gene annotation resources for genes of specific interest. BioGPS was developed to meet the needs of both academic and commercial organizations. It runs searches for human, mouse, and rat genes. Andrew Su, a senior research investigator in computational biology at the Novartis Research Foundation, told BioTechniques that the two most notable elements of BioGPS are the unstructured plug-in interface for community extensibility and the customizable user interface.
“Say you do some sort of profiling experiment—a microarray, next generation sequencing, etc—and find that there are 10 candidate genes highlighted in your study. How do you learn what's known about these genes?” asked Su. “There are hundreds of public gene-centric resources available, and many organizations also have internal databases with proprietary gene annotation information. The problem that BioGPS addresses is how to aggregate data from all these separate online databases into one application and interface.”
“We won't go so far as to say BioGPS is a replacement for any other tool that's out there,” said Su. “Rather, we view BioGPS as a new tool that is complementary to existing resources. But we definitely feel that the design principles behind BioGPS and the emphasis on 'community intelligence' are unique among gene annotation databases.”
BioGPS’ gene annotation database is comprised of information from public sources and data generated by the Novartis research group. The search interface allows researchers to look for genes based on most public identifiers. The portal utilizes a simple plug-in interface in HTML language that enables most gene-centric external databases to be included in BioGPS, and any registered user is allowed to add plug-ins, said Su. Currently, BioGPS has over 250 plug-ins spanning 100 unique domain names.
Researchers can customize the way the portal presents information to highlight the most relevant resources. “Most gene-centric databases tell the user what they think the user should know about their gene of interest. In contrast, BioGPS allows users to individually combine and arrange plug-ins into layouts, enabling each user to define for themselves what content they find most useful,” said Su.
The paper, “BioGPS: an extensible and customizable portal for organizing and querying gene annotation resources,” was published on Nov. 17 in the online edition of Genome Biology.