Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Germinate: A Plant Data Management System

Jennifer M. Lee¹ , Guy Davenport^2,5 , David Marshall³ , T.H. Noel Ellis² , Michael J. Ambrose² , Jo Dicks² , Theo J.L. van Hintum⁴ , Andrew J. Flavell¹

¹  University of Dundee, Department of Life Sciences, Dundee, DD1 4HN, Scotland UK

²  John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

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

⁴  Centre for Genetic Resources, P.O.Box 16, 6700AA Wageningen, The Netherlands

⁵  (GD current address) CIMMYT, El Batan, Texcoco, Mexico

GERMINATE (http://bioinf.scri.sari.ac.uk/germinate/) is a general plant database designed to hold data types ranging from molecular data to phenotypic data for any plant species. GERMINATE has been specifically designed to cope with varying ploidy levels found among plants. Its main purpose is to integrate molecular data (e.g. marker data) with descriptive data (e.g. geographical, passport, morphological) for large germplasm or genotype collections. GERMINATE uses a top level Accession entry ID to allow association and querying between disparate sets of data associated with an accession. We have initially tested GERMINATE with pea, wheat, barley, and lettuce at the partner institutions. GERMINATE has now been distributed to interested collaborators for testing in a broader range of species with a wider variety of data. This includes members of the Generation Challenge Program Consortium who are testing GERMINATE for use with species such as rice, potato, and maize. We are also testing various types of interfaces to GERMINATE, from a light-weight perl-cgi interface designed for data retrieval to more complex java based interfaces which would allow analysis as well as data retrieval. We also expect to make the data in GERMINATE available as a web service interface so it will interact well with tools being developed by collaborators. GERMINATE is currently being implemented in the public domain PostgreSQL and is available under the GNU GPL. We envisage that this will form an ideal platform to enable us and other groups to develop a range of interfaces and analysis tools to interact with the database.