Phänotypisierungen

A tool for simple and fast phenotyping in plant sciences

Projektbeschreibung

Plant breeding and genetics require fast and exact phenotyping that is reproducible independent of scientist and location. Efficient statistical evaluation furthermore requires standardized data storage. Safe data storage must ensure long-term availability of data, ideally over organizational barriers while maintaining intellectual property rights. All this is already state of the art at large phenomics centers. However, these resources are unavailable for most scientists. For these, we develop a simple and cost-efficient system that employs mobile data recording systems for onsite data entry. The system uses personal digital assistants (PDA) to enter phenotyping data on-site into user defined forms, so called ‘phenotyping schemes’. These schemes can be defined by the user on a web-based graphical user interface ‘Test Program Composer’ from controlled vocabulary compatible with published ontologies (e.g. the plant ontology consortium). XML-based downloads of the phenotyping scheme from the webpage allow easy transfer to the recording system and exchange between users. On the terminal, the interface ‘Mobile Phenotyper’ displays the schemes and stores recorded data in XML and CSV format. For long-term data storage, data can be uploaded to data management pipeline based on the systems developed for the TROST project (Billiau et al. 2012 http://dx.doi.org/10.1071/FP12009). Within that pipeline, web tools store the original data files, upload data from the mobile device into the standardized storage format of a database and provide download tools. Aiming for an open source, low cost solution, we used free software components for database (MySQL) and website (Apache Tomcat, Apache httpd2 webserver, CakePHP). After field testing in 2012 by academic groups and breeding companies, we built a web-based distribution and user support system to make the system available to a wider community. Along that line, we increased the portability of the system to different types of mobile devices and to different operating systems. Presently, we are recruiting a large user population to establish a self-sustaining system for the scientific community.