Germinate Summary

Germinate is a generic plant data management system implemented in MySQL and designed to hold passport data and a range of additional data types including molecular markers. Its use of a top level Accessions entry ID allows association and querying between disparate sets of data associated with an accession.

The database is implemented in the public domain with MySQL relational database management system and it is freely available under the terms of the GNU public license. We envisage that this will form an ideal platform to enable us and other groups to develop a range of standard interfaces and analytical tools to interact with the underlying database.

The new Germinate Database version 2.0 is now available for download and evaluation. Detailed descriptions of the features and capabilities of Germinate 2.0 are provided in the accompanying documentation.

For further information please contact us at germinate@scri.ac.uk .

This work has been supported by the BBSRC Grants 94/BEP17084, BB/E003184/1 and SEERAD FF00589 as part of the Bioinformatics and E-science program.

Overview

The genetic resources community has put huge amounts of effort into systematically generating, gathering and storing plant data in collections. The motivation for these efforts is to quantify and preserve genetic diversity in plants and facilitate the selection of germplasm for utilisation in breeding projects (http://www.bioversityinternational.org and http://www.ars-grin.gov/npgs). In order to combat new environmental stresses as they are encountered and to ensure future food security, it is vital to use the biodiversity that has been so carefully preserved in these germplasm collections. The characterization and analysis of plant genetic resources are integral to the usefulness of germplasm collections. New approaches to maintaining and analysing genetic resources, alongside the technological advances made within the genomics revolution, have resulted in the generation of substantial amounts of data of varying types for many plant species. However, most plant databases hold limited subsets of data and do not offer many opportunities to link between the different types of data, limiting the investigations which can be carried out on the germplasm.

Through a collaborative effort we are developing the Germinate Database. The primary goal of Germinate is to develop a robust database which may be used for storage and retrieval of a wide variety of data types for a broad range of plant species. Germinate focuses on genotype, phenotype and passport data, but has been designed to potentially handle a much larger range of data including, but not limited to ecogeographic, genetic diversity, pedigree and trait data, and will permit users to query between these different types of data. We have aimed to provide a versatile database structure, which can be simple, require little maintenance, may be run on a desktop computer, and yet has the potential to be scaled to a large, well-curated database running on a server. The design of Germinate provides a generic database framework from which interfaces ranging from simple to complex may be used as a gateway to the data.

The data tables are structured in a way that we are able to hold information ranging from simple data associated with a single accession or plant, to complex datasets, images and detailed text information. Features of the Germinate database structure include its ability to access any information associated with a group of accessions and to relate different types of information through their association with an accession.

The Germinate database is currently divided into numerous sub-schemas, which are designed to be bolt-on/off units although the database is always distributed with all schemas present. Schemas can be added or removed by the user to create the database most suited to their needs, or exported with minimal adaptation to other databases. This recognizes the reality that there are many databases in the genetic resources community and there never will be a consensus database in universal use.

Participants

The following is a list of the collaborators involved in developing Germinate 2.0

• SCRI
• University of Dundee
• John Innes Centre

About Germinate

Germinate was first released in 2004 as a collaborative project between SCRI, Dundee University and the John Innes Centre in the UK. (Lee, JM, Davenport, GF, Marshall, D, Ellis, THN, Ambrose, MJ, Dicks, J, van Hintum, TJL and Flavell, AJ (2005) GERMINATE - A Generic Database for Plant Genetic Resources Plant Physiology 139: 619-631). The initial database design was implemented by Jennifer Lee (UoD) who is now at UC Davis, California.

Germinate was initialy developed in PostgreSQL and used a web interface written in Perl. There was a substantial code base implemented to load data into the database using PostgreSQL.

In late 2006 work began on a new version of Germinate (Germinate 2.0) which would remove the limitations imposed by reliance on PostgreSQL and would allow the system to be run on a number of database systems. The initial prototypes were developed using MySQL, primarlily due to the expertise on offer at SCRI using this system and to cater for a large number of end users who were more familiar with the MySQL database engine. Although not fully tested it is envisaged that we now have a database independant platform. Currently we have a Perl front end to Germinate and are actively developing new tools and features for our web-users. In addition we also have a web-services interface in development as well as administration tools written in Perl and Rails which will aid users in configuring and maintaining data and Germinate installations.

The first Germinate 2.0 database was released on the 29th March and hosted 180 000 accessions from the Potato, Wheat and Aegilops collections from the CGN centre in Wageningen, Netherlands under the BioExploit project.

To view some examples of Germinate databases visit our websites section or drop us an email on bioinf@scri.ac.uk