In order to ensure consistent reliability and accessibility of the BioGRID web interface, we have migrated the BioGRID to a cloud-based server system with a third party provider that provides up-to-date hardware, facile operating system upgrades and improved fault tolerance. BioGRID 3.2 supports ~28 million systematic names, aliases, official symbols and external identifiers from Ensembl (30
), UniprotKB (31
), NCBI Entrez-Gene (32
), Genbank (33
), SGD (13
), WormBase (23
), FlyBase (26
), HGNC (34
), MGD (27
), TAIR (15
), VectorBase (35
), BeeBase (36
), ZFIN (25
) and HPRD (37
), among other sources. BioGRID currently also supports annotation for more than 85 organisms and contains interaction data for more than 30 different species. The BioGRID web service (webservice.thebiogrid.org) has been completely redesigned to run off the new decentralized database architecture for better access and maintenance by developers. The new web service will facilitate the incorporation of BioGRID data in other databases and applications. Additional new documentation in the BioGRID wiki provides comprehensive instructions for this resource.
The BioGRID 3.2 web interface has been upgraded to include an integrated post-translational modification (PTM) viewer. This viewer highlights PTM sites on protein sequences and incorporates much of the functionality available in PhosphoGRID (). PTM sites are colored within protein sequences according to the modification type, with clickable functions that display details such as publications, evidence codes and enzymatic relationships. The BioGRID currently supports both phosphorylation and ubiquitination sites and will expand to cover other major PTMs across all supported species.
Figure 2. PTM display features. (A) Button to reveal PTM sites. (B) Statistics for different types of PTMs. (C) Pop-up with links to publications that document PTM evidence and relationships. (D) Tabular view of PTM site locations and links to publications. (E (more ...)
To facilitate exploration of the biological datasets in BioGRID, we have developed a new gene tag feature for specific annotation, including membership in network-specific cohorts, gene functions or detailed attributes such as PTM site information. These gene tags can be used to build customized datasets for downloads and to define criteria for building and maintaining project-specific datasets, as for example defined by themed curation projects. These datasets may be maintained in concert with monthly BioGRID updates and are subject to strict version controls that allow reference to specific builds for data analysis. Project-specific datasets—such as for the CM and UPS datasets—will be accessed through custom gateways within the BioGRID that encompass genes, interactions, publications and biological context for the project.
Graphical network representation provides an intuitive summary of an interaction query dataset and, when appropriately configured with a dynamic interface, can be used to inspect and further query a network of interest. However, a drawback of current network visualization software is that the graphical output becomes cluttered as network complexity increases. To address this issue, we have developed a new dynamic BioGRID interaction viewer that is based on a simple visual layout and which has user-friendly filters (). In the BioGRID viewer, all interaction nodes are distributed in a circular layout with the query gene in the center. The properties of individual interactions are visualized by moving the tooltip over the interactor of interest to highlight gene information, including species type, gene acronym, gene identifier and number of interactions in BioGRID. To facilitate retrieval of data types of interest, the viewer provides the user with a check-box filter to reduce the complexity of the graph. The user can thus choose to view only those interactions supported by particular types of experimental evidence, low- versus high-throughput data or species-specific data. The network can also be extended to include all known interactions between interactors for the query. Results of the filtered and/or extended query are downloadable in tab2 format with a single click. The BioGRID viewer is based on an open source widget, downloadable from GitHub (https://github.com
), and is embeddable in any web page. Network images in the viewer are rendered from interactions retrieved from the BioGRID REST service. The viewer is implemented using the d3js (http://d3js.org/
Figure 3. The BioGRID viewer. (A) In the example shown the viewer returns all the interactions of the query gene/protein and interactions between the hit genes/protein. Properties of individual interactions are revealed by hovering over the interaction node of (more ...)