Plant & Animal Genome IX Conference

Workshop: Bioinformatics/Computers
W15_06.html

UK CROPNET: INTEGRATING AND ANALYSING DATA FROM DISTRIBUTED SOURCES

¹ John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

² NASC, Division of Plant Science (UP), University of Nottingham, Nottingham, NG7 2RD, UK

³ Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

⁴ USDA-ARS and Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA

⁵ Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK

The UK CropNet Bioinformatics Network (UK CropNet, http://ukcrop.net/) was established in 1996 and is now in its second phase of funding, with continued support from BBSRC. The UK CropNet WWW server gives online access to the Arabidopsis Genome Resource (AGR), BarleyDB, BrassicaDB, FoggDB (forage grasses) and MilletGenes (pearl, foxtail and finger millets) databases as well as many crop plant databases from our US partners. At present, it is difficult to analyse data from more than one database at a time. One of the priorities of UK CropNet has been the development of an infrastructure to allow simultaneous querying of multiple databases using comparative information. ARCADE (A Real-time comparative analysis display environment - http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/ARCADE/) is a new computer tool that will provide such a comparative infrastructure. It is currently in a prototype version but will be developed further throughout 2001. ARCADE supports two types of data interrogation. Firstly, speculative queries such as Find me all entities in wheat and foxtail millet that are associated with yield may be made. Secondly we may wish to make queries such as Tell me the location of the homologue of Arabidopsis gene A in Brassica napus, which relies on pre-defined comparative information stored in a database called ComapDB. At present ARCADE connects to databases that use the ACEDB database management system (the majority of crop plant databases). However, we intend to widen its scope in future to include many more public databases containing crop plant data (e.g. sequence databases).