Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract BioGPS (The Gene Portal Hub) is a free extensible and customizable ‘gene annotation’ portal, a complete resource for learning about gene and protein function.

BioGPS is based on a loose federation of existing genetic and genomic resources. It allows users to easily explore the landscape of gene annotation resources for one or more genes of interest. BioGPS currently focuses on annotation for human, mouse, and rat genes.

BioGPS also emphasizes two (2) key design features. First, BioGPS is based on a simple, unstructured plug-in interface that allows for simple community extensibility.

Second, BioGPS also implements an advanced user interface that enables precise user customizability.

In sum, these two design principles enable BioGPS to harness the principle of ‘community intelligence’ toward the goal of efficiently organizing and querying online gene annotation resources.

BioGPS Basic gene portal functionality --

Like many online gene annotation resources, BioGPS maintains a ‘gene annotation database’ that combines information from public sources with data generated by the manufacturer.

Scientists can find their gene or genes of interest using a flexible search interface, which accepts most public gene identifiers (Entrez Gene, Ensembl, RefSeq, UniProt, Affymetrix, etc.) and gene annotation identifiers [Gene Ontology (GO), Interpro], as well as coordinates of a ‘genomic interval’.

Selecting a gene out of the search result list displays a gene annotation report. In the case of BioGPS, the default ‘gene annotation report’ focuses on the manufacturers reference ‘Gene Atlas’ data sets, which show ‘gene expression patterns’ from a diverse set of tissues and cell types.

BioGPS provides several other gene report layouts that correspond to other common use cases. Each layout is an arrangement of ‘plug-ins’, and plug-ins primarily rely on third-party websites for content.

For example, the ‘Reagents’ layout contains several plug-ins, each of which shows the ‘molecular biology’ reagents available from a commonly used reagent provider.

The ‘Literature’ layout focuses on literature searching, displaying plug- ins for both PubMed and Google Scholar. The ‘Model Organism Databases’ layout shows plug-ins for the Mouse Genome Database (MGD) and the Rat Genome Database (RGD) sites.

The ‘Wikipedia’ layout shows the ‘Gene Wiki’ plug-in (A gene wiki for the community annotation of gene function).

The ‘KEGG’ layout shows biological pathways relevant to any particular gene of interest.

Finally, the ‘Exon Atlas’ layout displays a plug-in showing data for a previously unpublished reference expression data set using a mouse exon array.

Depending on which gene annotation resources are most relevant, a user can easily switch between layouts using a simple drop-down menu.

The layout system allows users to easily and directly view gene-centric data from multiple online data sources without having to initiate a query at each site. Although BioGPS often provides easy access to a site's basic ‘gene report’ page, drilling deeper into a given site still requires more specific knowledge of each site's unique navigation and search features.

BioGPS community extensibility via a simple, unstructured data format --

BioGPS itself hosts a relatively limited amount of gene annotation data, and the majority of content is obtained through its role as a ‘content aggregator’ of other online gene annotation resources.

BioGPS utilizes a virtually unstructured format for integrating disparate gene annotation resources. This data format is the simplest online format available - HyperText Markup Language, or HTML.

Using simple HTML interfaces, BioGPS interacts with users and third- party plug-in providers. BioGPS maintains a plug-in library that stores a Uniform Resource Locator (URL) template for each registered plug-in.

This simple HTML-based data sharing mechanism allows most existing online tools to be easily integrated as BioGPS plug-ins, and it also allows new resources to be packaged as BioGPS plug-ins with minimal additional effort.

The BioGPS plug-in library currently has over 150 ‘registered plug-ins’. The selection of plug-ins spans many different areas and resources, including literature searching, model organism databases, genetics resources, pathways tools, and reagent providers (as stated above...).

These online resources span over 65 unique domain names, indicating the relative ease with which existing resources can be registered as BioGPS plug-ins.

In addition, BioGPS hosts a ‘gene expression’ plug-in that displays reference ‘expression patterns’ from the Gene Atlas data sets and expression quantitative trait loci (eQTL) studies, as well as new data sets for an updated mouse Gene Atlas [GEO:GSE10246] and exon array atlas [GEO:GSE15998].

BioGPS user customizability using layouts --

Since BioGPS provides a ‘simple mechanism’ by which online gene annotation resources can easily be registered as plug-ins, the BioGPS user interface is critical for its utility to users.

BioGPS utilizes a technically simple user interface. All plug-ins are rendered in IFRAMEs, which are essentially ‘web browsers’ embedded within a main web browser.

In this way, BioGPS is truly a federated hub, providing users’ browsers with deep-links into plug-in servers based on the URL template. Plug-in content is returned and rendered using simple HTML.

BioGPS custom layouts capability enables each user to tailor BioGPS to their individual interests using any of the registered plug-ins in the plug- in library.

Within a layout, plug-ins are visualized using a ‘windowing framework’ in which, similar to common operating systems, windows can be repositioned and resized using standard click-and-drag mouse actions. Switching between layouts (either pre-defined or personalized) can be done using a simple drop-down menu.

BioGPS is openly and freely accessible online. Users can optionally register for a user account to enable ‘customization features’, and registration is also completely free. Screen-cast tutorials can be found in the Help section.

BioGPS Software architecture --

BioGPS was built following a three-tiered application model. The data tier was implemented using Oracle, and data tables were populated by importing gene annotations and relationships from common ‘gene annotation databases’ (predominantly NCBI and Ensembl).

The business logic tier was built using C# and the .NET Framework, utilizing the Windows Communication Foundation (WCF) to expose Representational State Transfer (REST)-based web services for querying and data retrieval.

The presentation layer, which includes the plug-in and layout management system, was built using the Django web framework and extensively uses the EXTJS JavaScript library.

Note: BioGPS is now an app for iPhone® and iPod touch®!

System Requirements



Manufacturer Web Site BioGPS

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G6G Abstract Number 20546

G6G Manufacturer Number 104161