title: 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.
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA vkrishna@jcvi.org.
authors.forename: Vivek
authors.identifier: http://orcid.org/0000-0002-5227-0200
authors.initials: V
authors.lastname: Krishnakumar
authors.affiliation: Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA.
authors.forename: Matthew R
authors.identifier: http://orcid.org/0000-0003-1851-4862
authors.initials: MR
authors.lastname: Hanlon
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK.
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Erik S
authors.initials: ES
authors.lastname: Ferlanti
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Karamycheva
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Maria
authors.initials: M
authors.lastname: Kim
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Rosen
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Chia-Yi
authors.initials: CY
authors.lastname: Cheng
authors.affiliation: Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA.
authors.forename: Walter
authors.identifier: http://orcid.org/0000-0001-9454-441X
authors.initials: W
authors.lastname: Moreira
authors.affiliation: Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Mock
authors.affiliation: Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Stubbs
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK.
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sullivan
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Krampis
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK.
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
authors.affiliation: Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA.
authors.forename: Matthew
authors.identifier: http://orcid.org/0000-0002-1384-4283
authors.initials: M
authors.lastname: Vaughn
authors.affiliation: Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D057225:Data Mining; D030541:Databases, Genetic; D018745:Genome, Plant; D020407:Internet; D012984:Software