Arabidopsis Information Portal (Araport)
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.
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.
The Plant journal : for cell and molecular biology. 2017-02-01; 89.3: 789-804.
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Plant & cell physiology. 2017-01-01; 58.1: e4.
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery
Nucleic acids research. 2015-01-01; 43.Database issue: D1003-9.
Araport: the Arabidopsis information portal
The Plant cell. 2012-06-01; 24.6: 2248-56.
Taking the next step: building an Arabidopsis information portal
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).