The Arabidopsis Informational Portal

Purpose

The Arabidopsis Information Portal (Araport) is an NSF and BBSRC-funded collaborative project between the J. Craig Venter Institute, TACC, and the University of Cambridge. It is an open-access online community resource for Arabidopsis model plant research. AIP enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation including gene structure, gene expression, protein function, and interaction networks, all via a single interface.

The project also provides an extensible framework for incorporation of new data sources and creation of user interfaces to consume them. It uses a data warehouse (InterMine) to provide a searchable index of sequence-associated data, which is supplemented data federation to deliver in-depth information at run time. AIP relies on the community to contribute modules that extend its functionality. Modules can present federated data (obtained via RESTful web services) with in-browser visualization software (JavaScript, jQuery, etc.). To support data federation, AIP uses innovative middleware based on the iPlant Agave platform to support enrollment, discovery, and access to community-developed web services within a unified framework. AIP incorporates and integrates GMOD genomics applications including InterMine, JBrowse, GBrowse, WebApollo, Tripal, and Chado. The AIP project is fully open source, maintaining an active GitHub repository and virtual organization structure. AIP hosts tutorials, workshops, and hackathons to help the community enrich and exploit this resource. Designed for sustainability, the AIP strategy exploits existing scientific computing infrastructure, adopts a practical mix of data integration technologies, and encourages its user community to contribute suggestions, data sets, web services, and software.

Funding Source(s)

• NSF ABI-1262414
• BBSRC BB/L027151/1

Related Links

• The Arabidopsis Information Portal
• iPlant Collaborative
• Agave API
• Intermine
• Generic Model Organism Database