Araport: the Arabidopsis information portal.

Vivek Krishnakumar,Christopher D Town,Sergio Contrino,Maria Kim,Benjamin D Rosen,Erik S Ferlanti,Julie M Sullivan,Jason R Miller,Gos Micklem,Stephen A Mock,Matthew Vaughn,Chia-Yi Cheng,Svetlana Karamycheva,Joseph Stubbs,Walter Moreira,Matthew R Hanlon,Konstantinos Krampis

doi:10.1093/nar/gku1200

Vivek Krishnakumar, Christopher D Town + Show 15 more

Open Access

https://doi.org/10.1093/nar/gku1200

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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.

Highlights

The flowering plant Arabidopsis thaliana is a model organism for molecular, cellular and systems biology
The Arabidopsis Information Resource (TAIR) served as the collector, curator and provider of pertinent information centered on the reference Col-0 genome
In 2009, the Arabidopsis community was faced with a growing number of online resources and potential loss of its central organizing resource, TAIR

Summary

Introduction

The flowering plant Arabidopsis thaliana is a model organism for molecular, cellular and systems biology. It offers two core web applications: ThaleMine for data mining and JBrowse for genome browsing. The core of AIP is a database of basic genomic data within a data mining web application called ThaleMine.

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