Plant Cell. 2010 Aug;22(8):2530-6. doi: 10.1105/tpc.110.078519. Epub 2010 Aug 31.
An international bioinformatics infrastructure to underpin the Arabidopsis community.
Bastow R, Beynon J, Estelle M, Friesner J, Grotewold E, Lavagi I, Lindsey K, Meyers B, Provart N, Benfey P, Birney E, Braun P, Brendel V, Buell R, Caccamo M, Carrington J, Cherry M, Ecker J, Eppig J, Forster M, Gutiérrez R, Hilson P, Huala E, Katari M, Kersey P, Kudla J, Ma H, Matsui M, Matthews K, May S, Mayer K, Millar A, Millar H, Mjolsness E, Mockler T, Nikolau B, Nordborg M, Rawlings C, Schofield P, Schoof H, Schroeder JI, Sen TZ, Stanzione D, Town C, Toyoda T, Vision T, Walsh S, Wang X, Ware D, Weckwerth W, Yang W.
Abstract
The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee and the North American Arabidopsis Steering Committee. There are extensive tools and resources for information storage, curation, and retrieval of Arabidopsis data that have been developed over recent years primarily through the activities of The Arabidopsis Information Resource, the Nottingham Arabidopsis Stock Centre, and the Arabidopsis Biological Resource Center, among others. However, the rapid expansion in many data types, the international basis of the Arabidopsis community, and changing priorities of the funding agencies all suggest the need for changes in the way informatics infrastructure is developed and maintained. We propose that there is a need for a single core resource that is integrated into a larger international consortium of investigators. We envision this to consist of a distributed system of data, tools, and resources, accessed via a single information portal and funded by a variety of sources, under shared international management of an International Arabidopsis Informatics Consortium (IAIC). This article outlines the proposal for the development, management, operations, and continued funding for the IAIC.
- PMID:
- 20807877
- [PubMed - indexed for MEDLINE]
- PMCID:
- PMC2947164
Free PMC ArticleFigure 2.
The Structure of the IAIC.
IAIC consists of core of four components in blue: (1) the AIP, which is the central hub of the consortium, provides a single user interface to access to all the constituent parts of the consortium, sets standards, and provides training; (2) gold standard genome annotation; (3) curation of functional data; and (4) stock center database(s) to enable rapid access to resources. Noncore modules are illustrated in purple; those listed in the figure are just examples and are not meant to be an exhaustive list. The comparative genomics module (in green) provides one example of how the IAIC will link out to other plant species.
Plant Cell. 2010 August;22(8):2530-2536.
Figure 1.
Three Tiers of Data Resources.
Proposed scope for an information resource to house interpreted biological resources (modified from Parkhill et al., 2010). The lowest and most fundamental tier consists of local databases of specialized data resources run mainly by individual investigators. The second tier provides a layer of consolidation into more durable and useable forms for a larger defined community; an Arabidopsis community portal belongs in this level and is indicated as AIP. The third tier enables cross-species comparisons; this requires an integrated set of diverse resources.
Plant Cell. 2010 August;22(8):2530-2536.
Figure 3.
Management Structure of the IAIC.
The management of the IAIC is split into three levels. (1) IAIC Committee consisting of the PIs leading the core components and noncore modules of the IAIC. This committee would report to and interact with the SAB. (2) SAB, consisting of a minimum of one scientist from each of the countries involved in the IAIC. The SAB would oversee the development of the IAIC and interact with the funding agencies, MASC, and the community. (3) SAP, which would review the progress of the IAIC.
Plant Cell. 2010 August;22(8):2530-2536.
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