Taking the next step: building an Arabidopsis information portal

Abstract

The Arabidopsis information portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.

Figure 1.

Main Components of the AIP, Version 1.0. An overview of the user needs that the AIP will be designed to satisfy, including the basic functionalities to be built into the initial release of the portal.

Figure 2.

Examples of Module Contributions to the AIP. Modules can be built on existing infrastructure, consolidation, and investigator tier databases. Some modules, denoted with dark gray backgrounds, are ready to be integrated into the AIP immediately, while those with medium to light gray backgrounds would require further development to be part of the AIP. As an example, arrows denote lines of communication activated by adding a Comparative Genomics module visualized with a Tree Visualizer app to a user's workspace for a gene of interest. Other modules would communicate with each other or with the depicted external databases if a user selected it to appear on his/her workspace. Note that the databases listed do not constitute a complete list; many that could be added were omitted due to space limitations.

Figure 3.

The Planned Transition from TAIR to AIP, Including a Transitional Period in Which TAIR Resources Are Housed at iPlant. The coming years are indicated on the horizontal axis, including the next two planned International Conferences on Arabidopsis Research (ICAR). The timing of the transition of TAIR to the iPlant servers, and the development of the AIP, is indicated above.