Extending Tripal to manage banana genetic resource information

Abstract

Large-scale genetic and phenotypic characterization of germplasm collections has the great potential to change the way scientists deal with genetic resources. Users of genebanks should be in a position to select germplasm material based on a combination of passport, genotypic and phenotypic information among the global genepool. A new generation of information systems has to be designed to efficiently handle this information and link it with others external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS) addresses the management of banana genetic resources. It is implemented with Drupal content management system using the Tripal module to work with Chado database schema. However, this stack does not address completely all of our requirements. It should allow us to handle access restriction, germplasm ordering, workflows and should track all changes for quality control. Finally, there is a need for interoperability among external resources or fieldbooks. Fortunately, Drupal and Tripal have been designed to support custom extensions like the ones we created. Firstly, the Chado Controller extension manages Chado data access levels, modification history and data integrity checks. The Multi-Chado extension brings more control over data access and enables the use of other Chado instances on a same Tripal instance. Then, the Breeding API extension enables data exchange with external systems. Finally, an additional in-house extension called MGIS module gives us even more flexibility.