AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

Extending Tripal to manage banana genetic resource information

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