Arabidopsis Information Portal (Araport)

Arabidopsis Information Portal (Araport)

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The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport integrates gene structure with public data from TAIR, UniProt, PubMed, BAR, EPIC-CoGe, and other sources and 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. Araport offers a single interface through which to access a wide range of Arabidopsis information. Araport produced and hosts an updated version of the annotation of the Arabidopsis thaliana Col-0 reference genome sequence, named Araport11 that includes splice variants computed with tissue-specific transcript assemblies from over 100 RNA seq data. Araport annotation will incorporate community curation facilitated through the Araport web site. Araport users can query and view gene structure data including ThaleMine (an Arabidopsis-specific instance of InterMine), and  JBrowse. In ThaleMine, users can not only save results but manipulate them, visualize them, and expose them as web services.

Araport 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. Araport relies on data federation to deliver in-depth information at run time. Araport 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, Araport uses innovative middleware based on the iPlant Agave platform to support enrollment, discovery, and access to community-developed web services within a unified framework. Araport incorporates and integrates GMOD genomics applications including InterMine, JBrowse, GBrowse, WebApollo, Tripal, and Chado. The Araport project is fully open source, maintaining an active GitHub repository and virtual organization. Araport hosts tutorials, workshops, and hackathons to help the community enrich and exploit this resource.

In all, the Araport 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.

Publications

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
The Plant journal : for cell and molecular biology. 2017-02-01; 89.3: 789-804.
PMID: 27862469
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.
Plant & cell physiology. 2017-01-01; 58.1: e4.
PMID: 28013278
Araport: the Arabidopsis information portal.
Nucleic acids research. 2015-01-01; 43.Database issue: D1003-9.
PMID: 25414324

Funding

The Arabidopsis Information Portal is funded by a grant from the National Science Foundation (#DBI-1262414) and co-funded by a grant from the Biotechnology and Biological Sciences Research Council (BB/L027151/1).