Award details

Arabidopsis Stock Centre Module.

Reference	BB/L010100/1
Principal Investigator / Supervisor	Professor Sean May
Co-Investigators / Co-Supervisors
Institution	University of Nottingham
Department	Sch of Biosciences
Funding type	Research
Value (£)	638,396
Status	Completed
Type	Research Grant
Start date	02/01/2014
End date	01/01/2018
Duration	48 months

Abstract

This proposal requests support for survival and curational expansion of our current database and e-commerce site; with significant core changes and updates associated with increasing federation, fluid partnerships and local/remote virtualisation. Primary objectives: 1. Continue and maintain informatic operations for our germplasm distribution centre including ongoing curation of stock additions (~20K per year). 2. Develop state of the art federated data integration based on existing infrastructure and experience. Our current germplasm database and catalogue are MySQL, Apache, Perl & Python on RedHat with internal curation through Servoy API (Java) and command line scripts; plus Visual Basic pre-filtering of data. We have an AMIGO tree browser based on PO/PATO (EAV variant) for a subset of data with some ecotypes served through GoogleMaps (KML and live). Financial cost-recovery operations are UoN bespoke (Generic Payment Pathway ; WorldPay - scheduled to change provider in 2013) connected to our internal e-commerce catalogue. Some data has already been migrated into iplant (development not deployed) and we are working on local virtualisation to support migration out of existing hardware into UoN central repositories. Our legacy locus/genomics data associated with stocks are in MySQL served via XML (by XSLT) and DHTML / JavaScript plus legacy external ensembl and internal Gbrowse / CHADO with script-automated curation updates. Current NASC Web Services (120+) are SOAP2 (and legacy BioMOBY) with initial RESTful conversions in progress. TAIR closes this August. To be a core provider to the federated AIP that replaces TAIR and to maintain our services, we need to consolidate our data management approaches listed above; and capitalise on our early adoption of critical standards. We are already well placed in expertise and services, but the next few years will see significant change and we need to maintain our development impetus to stay functional.

Summary

NASC is a seed and data resource that emerged consensually out of the community 20 years ago and services a vigorous worldwide Arabidopsis community in collaboration with our sister centre ABRC in the USA. Our resource is widely used and appreciated globally as shown by our distribution statistics (between 50-100,000 stocks per year over the last 5 years sent all over the world from each centre). Our users extend from crop scientists and biologists through to mathematicians and system biologists. We are referenced in a very large number of publications as an underpinning resource for plant sciences, and have helped scientists to receive essential materials in a very cost effective, straightforward, consistent and efficient manner for two decades. As required by the BBSRC, we run the NASC stock centre as a partial cost recovery service that charges small fees for seed and clone stocks in order to subsidise our operations. To do this we have an e-commerce system linked up to our internal germplasm data module. This proposal is for the informatics and bioinformatics of the catalogue, germplasm curation and data distribution. Primary objective : to continue and maintain informatic operations for our very busy (continually expanding and extending) germplasm distribution centre. Secondary objective : to use current state of the art integration technologies to stay relevant to changes and progress in the international arabidopsis resource provision community. Recent changes in the international Arabidopsis funding model have led the imminent closure (this August) of the central arabidopsis database resource TAIR in the USA. As a community we are being asked to share the responsibility for Arabidopsis data resources more generally across multiple sites of specialisation. NASC is a critical partner in the future 'federated' model for Arabidopsis informatics. Our germplasm resource has been separate from TAIR for ALL seed operations since 1991; so we are ready for this change. In addition, we were a founding member of earlier distributed resources within Europe (PLANet: framework V funding), and have prior experience and expertise in federation (internally and externally). This proposal would ensure continuity and stability of physical and germplasm data resources for the European Arabidopsis community (and beyond). Our past experience, current capabilities and strong positive ties with the US stock centre (ABRC) and the US Arabidopsis Informatics Portal (AIP), will allow us to lead this area internationally.

Impact Summary

The increasing demands of a growing, prosperous world for improved agricultural products including food, fibre and fuel, intensifies the need for an extensive understanding of the basic biology and ecology of plants. Arabidopsis is the most widely used model system to study plant biology and has delivered numerous breakthroughs in understanding of plant and basic biological processes. Knowledge gained from studies in Arabidopsis serves to advance our understanding of other plant species, particularly crop species, and thus translates into new or improved plant products and increased agricultural productivity. Arabidopsis has underpinned the genomic revolution in plant science and represents the template on which other plant and crop genomes are annotated and assessed. Arabidopsis data is key to modern crop science and through that to food security and quality of life. Filing of patents is one measure of potential commercial activity and in 2010 there were 1,137 US utility patents referencing Arabidopsis compared to only 23 in 1994. A similarly dramatic 35-fold increase in European patent applications referencing Arabidopsis has occurred in the same timeframe. According to The Arabidopsis Information Resource (TAIR); as of May 10th 2011 there were 21,771 Arabidopsis researchers in 8,465 laboratories worldwide. The Nottingham Arabidopsis Stock Centre (NASC) and our sister centre ABRC in the US, together have a vital core role as infrastructure support for this highly distributed and prolific Arabidopsis community. Our services are equally available to Universities, institutes, companies and international users through simple, intuitive interfaces. Distribution abroad requires the same infrastructure as a purely UK resource but adds value by encouraging international donation of stocks, supplementing grant income and helping to consolidate the Arabidopsis and wider plant Community. All European plant research groups requiring Arabidopsis stocks are obliged to useNASC (All American users are obliged to use ABRC); but thousands of non-Europeans access our resource, particularly from Asia (notably China). We provide materials, data and guidance worldwide and our existence helps tens of thousands of users to save time, money and effort through centralised services. Our outreach is extensive, regular and user- oriented and we constantly strive to improve both our customer service and our value to the community. We have also been useful to BBSRC policy makers and marketing units through our inclusion in BBSRC publications: the BBSRC Data Sharing Policy documentation held NASC up as one of four examples of good practice; the 2009 BBSRC Bioscience Resources for Food Security pamphlet specifically flagged us as a key collection seed resource and our transcriptome analysis service as supporting the UK Food Security priority. These documents are utilised both by science policy makers and strategic users.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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