TY - JOUR
T1 - Arabidopsis bioinformatics resources
T2 - The current state, challenges, and priorities for the future
AU - International Arabidopsis Informatics Consortium
AU - Doherty, Colleen
AU - Friesner, Joanna
AU - Gregory, Brian
AU - Loraine, Ann
AU - Megraw, Molly
AU - Provart, Nicholas
AU - Slotkin, R. Keith
AU - Town, Chris
AU - Assmann, Sarah M.
AU - Axtell, Michael
AU - Berardini, Tanya
AU - Chen, Sixue
AU - Gehan, Malia
AU - Huala, Eva
AU - Jaiswal, Pankaj
AU - Larson, Stephen
AU - Li, Song
AU - May, Sean
AU - Michael, Todd
AU - Pires, Chris
AU - Topp, Chris
AU - Walley, Justin
AU - Wurtele, Eve
N1 - Funding Information:
Workshop, are supported by the National Science Foundation
Funding Information:
This work was supported by the US National Science Foundation (MCB Award 1062348, made to the U.S. members of the IAIC Steering Committee). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Publisher Copyright:
© 2018 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.
PY - 2019/1
Y1 - 2019/1
N2 - Effective 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.
AB - Effective 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.
KW - Arabidopsis
KW - The Arabidopsis Information Resource
KW - informatics
KW - international collaboration
KW - portal
UR - http://www.scopus.com/inward/record.url?scp=85061839515&partnerID=8YFLogxK
U2 - 10.1002/pld3.109
DO - 10.1002/pld3.109
M3 - Article
AN - SCOPUS:85061839515
SN - 2475-4455
VL - 3
JO - Plant Direct
JF - Plant Direct
IS - 1
M1 - e00109
ER -