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Browsing by Author "Provart, Nicholas J."

Now showing 1 - 4 of 4
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    Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future
    Doherty, Colleen; Friesner, Joanna; Gregory, Brian; Loraine, Ann; Megraw, Molly; Meyers, Blake C.; Provart, Nicholas J.; Slotkin, R. Keith; Town, Chris; Assmann, Sarah M.; Axtell, Michael J.; Berardini, Tanya; Chen, Sixue; Gehan, Malia; Huala, Eva; Jaiswal, Pankaj; Larson, Stephen; Li, Song; May, Sean; Michael, Todd; Pires, J. Chris; Topp, Chris; Walley, Justin; Wurtele, Eve (Wiley, 2019-01-01)
    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.
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    Current status of the multinational Arabidopsis community
    Parry, Geraint; Provart, Nicholas J.; Brady, Siobhan M.; Uzilday, Baris (Wiley, 2020-07-01)
    The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community.
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    Vision, challenges and opportunities for a Plant Cell Atlas
    Jha, Suryatapa Ghosh; Borowsky, Alexander T.; Cole, Benjamin J.; Fahlgren, Noah; Farmer, Andrew; Huang, Shao-Shan Carol; Karia, Purva; Libault, Marc; Provart, Nicholas J.; Rice, Selena L.; Saura-Sanchez, Maite; Agarwal, Pinky; Ahkami, Amir H.; Anderton, Christopher R.; Briggs, Steven P.; Brophy, Jennifer An; Denolf, Peter; Di Costanzo, Luigi F.; Exposito-Alonso, Moises; Giacomello, Stefania; Gomez-Cano, Fabio; Kaufmann, Kerstin; Ko, Dae Kwani; Kumar, Sagar; Malkovskiy, Andrey; Nakayama, Naomi; Obata, Toshihiro; Otegui, Marisa S.; Palfalvi, Gergo; Quezada-Rodriguez, Elsa H.; Singh, Rajveer; Uhrig, R. Glen; Waese, Jamie; Van Wijk, Klaas; Wright, R. Clay; Ehrhardt, David W.; Birnbaum, Kenneth D.; Rhee, Seung Y. (eLife, 2021-09-07)
    With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.