Arabidopsis Information Portal

October 13, 2014
Arabidopsis Information Portal

The Arabidopsis Information Portal is an open-access online community resource for Arabidopsis 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. AIP was funded in 2013 and came on line in 2014. AIP already offers a single interface through which to access a wide range of Arabidopsis information. AIP will grow through contributions of other labs in the form of modules: data, computation, and visualization tools.

AIP is designed to grow with the Arabidopsis community by providing an extensible framework for incorporation of new data sources and creation of user interfaces to consume them. AIP relies on a data warehouse (InterMine) to provide a searchable index of sequence-associated data. AIP relies on 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. 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.