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

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.

Figure 1

Schematic representation of BioGPS. In step 1, the user loads the BioGPS site in a web browser and inputs a query (here, 'CDK2'). In step 2, the web browser transmits the query to the BioGPS server. In step 3, BioGPS resolves the query into a gene entity, and returns fully formed URLs for plugins in the plugin library. In step 4, the user's web browser retrieves content from the plugin providers for the gene of interest and renders it within the customizable BioGPS layout.

Figure 2

A partial list of BioGPS plugins. Valid URLs can be formed by substituting gene-specific variables in the URL templates above. For example, for the gene CDK2, {{Symbol}} = CDK2, {{EntrezGene}} = 1017 (or 12566 for mouse), {{EnsemblGene}} = ENSG00000123374, {{HGNC}} = 1771, {{HPRD}} = 00310, {{MGI}} = 104772, and {{RGD}} = 70486. Plugin URL templates can also utilize variables for Unigene ID, RefSeq transcript or protein IDs, Protein Data Bank (PDB) ID, and Online Mendelian Inheritance in Man (OMIM) accession.

Figure 3

Screenshot of a custom BioGPS gene report layout for the gene CDK2. Registered users can easily create custom layouts using any plugins in the plugin library. Each plugin is rendered within its own window that can be moved, resized, and maximized using standard controls.