Germinate is a generic plant data management platform implemented in MySQL and is designed to act as a scaffolding on which complex web-based applications can be developed to leverage information from experimentally derived data. Germinate currently handles phenotypic, genotypic and passport data. The system offers users a standard set of interfaces for interrogation, browsing and displaying of a number of data types and can be easily expanded to add custom functionality depending on the application being developed. It is hoped that Germinate can grow into a stable set of tools on which diverse datasets can be seamlessly integrated using the common platform making interrogation of data from disparate or diverse datasets simpler.

The ability to bring together data from different sources in order to better understand or validate data that is currently held is becoming increasingly important. As a validation exercise Germinate is already uncovering intrinsic problems with historical phenotypic data.

The modular design of Germinate is key to its use to a wider audience than that of the pilot datasets that we originally developed the system to work with. We have developed a number of databases based on the Germinate, each of which shows very different uses for the platform. Examples of these databases are detailed below;

Germinate CPC

The Germinate Commonwealth Potato Collection (CPC) database was developed using the common components that Germinate offers as well as customised and tailored solutions that better fitted the data types that were presented through this dataset. Along with standard passport type displays the Germinate CPC database also shows experimentally derived disease resistance data as well as photographs of many of the 1500+ accessions that are currently held. Germinate was used to create an integrated information point detailing the Commonwealth Potato Collection including how the collection is maintained and how it was collected along with the passport and disease resistance data associated with its members.

Germinate BioExploit
The Germinate BioExpliot database was developed under Framework 7 in collaboration with the Centre for Genetic Resources (CGN) in Wageningen, The Netherlands. This database contains basic passport data for in excess of 160 000 Triticum , 7200 Solanum and 7900 Aegilops accessions. Where available geographic data is plotted using the Google Earth and Maps API.

Diversity of Species in Germinate
Germinate currently stores information at SCRI on barley, potato, wheat, Aegilops and pea. We also have outside interest from groups working on chickpea, cowpea, oats and onion.

Data is stored in a central database onto which are layered components for viewing and browsing data in a standard web browser and for the extraction of data from the central database in a form suitable for use in down-stream analysis program such as the genotype and phenotype visualisation application Flapjack. Germinate acts as the middle man between raw experimental data and downstream analysis tools.

For more information on Germinate please visit our main Germinate page.