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Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

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dc.contributor.authorDoherty, Colleenen
dc.contributor.authorFriesner, Joannaen
dc.contributor.authorGregory, Brianen
dc.contributor.authorLoraine, Annen
dc.contributor.authorMegraw, Mollyen
dc.contributor.authorMeyers, Blake C.en
dc.contributor.authorProvart, Nicholas J.en
dc.contributor.authorSlotkin, R. Keithen
dc.contributor.authorTown, Chrisen
dc.contributor.authorAssmann, Sarah M.en
dc.contributor.authorAxtell, Michael J.en
dc.contributor.authorBerardini, Tanyaen
dc.contributor.authorChen, Sixueen
dc.contributor.authorGehan, Maliaen
dc.contributor.authorHuala, Evaen
dc.contributor.authorJaiswal, Pankajen
dc.contributor.authorLarson, Stephenen
dc.contributor.authorLi, Songen
dc.contributor.authorMay, Seanen
dc.contributor.authorMichael, Todden
dc.contributor.authorPires, J. Chrisen
dc.contributor.authorTopp, Chrisen
dc.contributor.authorWalley, Justinen
dc.contributor.authorWurtele, Eveen
dc.date.accessioned2021-10-15T12:37:50Zen
dc.date.available2021-10-15T12:37:50Zen
dc.date.issued2019-01-01en
dc.date.updated2021-10-15T12:37:46Zen
dc.description.abstractEffective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resources include reference genome sequence data and an ever-increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community-defined common standards for data and metadata, and accessible and user-friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics). Community-established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy-in and participation in its establishment and development to encourage adoption.en
dc.description.versionPublished versionen
dc.format.extent7 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN 109 (Article number)en
dc.identifier.doihttps://doi.org/10.1002/pld3.109en
dc.identifier.eissn2475-4455en
dc.identifier.issn2475-4455en
dc.identifier.issue1en
dc.identifier.orcidLi, Song [0000-0002-8133-3944]en
dc.identifier.otherPLD3109 (PII)en
dc.identifier.pmid31245752en
dc.identifier.urihttp://hdl.handle.net/10919/105395en
dc.identifier.volume3en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000509897600001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectLife Sciences & Biomedicineen
dc.subjectPlant Sciencesen
dc.subjectArabidopsisen
dc.subjectinformaticsen
dc.subjectinternational collaborationen
dc.subjectportalen
dc.subjectThe Arabidopsis Information Resourceen
dc.subjectInternational Arabidopsis Informatics Consortiumen
dc.titleArabidopsis bioinformatics resources: The current state, challenges, and priorities for the futureen
dc.title.serialPlant Directen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2018-12-04en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Durelle Scotten
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/School of Plant and Environmental Sciencesen

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