UK CropNet 99

¹ NASC, Division of Plant Science (UP), University of Nottingham, Nottingham, NG7 2RD, UK

² Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

³ USDA-ARS and Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA

⁴ John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

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

The UK Crop Plant Bioinformatics Network (UK CropNet: http://synteny.nott.ac.uk/) was established in 1996 as part of the BBSRC's Plant and Animal Genome Analysis special initiative. We have now entered the second phase of UK CropNet, with continued funding from BBSRC through to 2003. The new phase of UK CropNet signifies the maturity of the resource, with easy access to well-populated crop plant databases and a growing number of display and analysis software tools. The UK CropNet WWW server gives online access to the AGR (Arabidopsis), BarleyDB, BrassicaDB, FoggDB (forage grasses) and MilletGenes (pearl, foxtail and finger millets) databases through the AceBrowser (http://stein.cshl.org/AcePerl/AceBrowser/) interface to the ACEDB database management system (http://www.sanger.ac.uk/Software/Acedb/). The SpudBase (potato) and ComapDB (comparative mapping) databases are coming to the end of their testing periods and will become publicly accessible in the near future. In addition, we mirror the USDA-funded crop plant databases from our US partners (indeed our CerealsDB database forms a UK node to the USDA GrainGenes database), to give rapid access to the UK and EU research communities.

The UK CropNet software resource (http://synteny.nott.ac.uk/software.html) now boasts a growing number of data display tools. Here, we have standardised on both Java-based interactive displays and on CORBA. Many of our software tools can communicate with data sources via CORBA, greatly increasing their power and applicability. UK CropNet's CITA tool, a CORBA Interface To ACEDB (http://jiio10.jic.bbsrc.ac.uk/development/CORBA) allows communication with a variety of ACEDB databases independent of their underlying model schemata. Our new ARCADE tool (for which a prototype will shortly be available) uses CITA; with a new querying language (CQL) developed especially for comparative genome analysis; and a Display Engine to enable users to carry out highly complex queries and to analyse the results with interactive tools and displays.

In the coming year we plan to:

• Expand and enhance our underlying database curation and management;
• Introduce CITA interfaces to the UK CropNet displays, so that users will be able to carry out fully interactive analyses of our databases, enabled by our Java display modules;
• Launch the first version of ARCADE by the end of 2000;
• Develop new tools and make major enhancements to existing software.