Araport: the Arabidopsis information portal

Abstract

The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release 'modules' that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts 'science apps,' developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.

Figure 1.

A Gene report page showing: (A) attributes like standard gene locus identifier, symbols/synonyms, TAIR curator summary, confidence rating, etc. Other useful information is segregated into the aspects, as follows: (B) ‘Genomics’ showing gene structure information; (C) ‘Function’ displaying the Gene Ontology annotation; (D) ‘Proteins’ with links to the relevant protein records populated with data from UniProt; (E) ‘Homology’ listing the computed orthologs and paralogs across a diverse set of species; (F) ‘Interactions’ showing a visual representation of the genes’ physical/genetic interactions (tabular format is also available); (G) ‘Expression’ reporting gene expression levels based on AtGenExpress project data, also visualized using an embedded eFP view; (H) ‘Publications’ reports papers associated with the current gene; (I) ‘Links’ to other InterMine databases where homologs of the current gene exist, and external links to several important Arabidopsis and plant genomics data providers.

Figure 2.

(A) (i) List of tracks available via the hierarchical track selector; (ii) a link to access the faceted track selector; (iii) track display panel showing the currently selected tracks for viewing (green inset: track chosen from the faceted selector). (B) Faceted track selector offers a search and filtering interface to enable choosing tracks based on the experiment metadata. (C) File upload capability ensures privacy to view ones own datasets alongside the Arabidopsis genome, and flexibility to work with large datasets such as short read alignments.