Ein Werkzeug für einfache und schnelle Phänotypisierungen in den Pflanzenwissenschaften
Final Report Abstract
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 longterm availability of data, ideally over organizational barriers while maintaining intellectual property rights. All this is already state of the art at large phenomics centres. However, these resources are unavailable to most scientists. For these, we develop a simple and cost-efficient system that employs personal digital assistants (PDA) for onsite data entry. A graphical user interface (GUI) on the PDA replaces the classical paper-based table. To maintain flexibility, the user defines his phenotyping schemes in the web-tool ‘Test Scheme Composer’. The schemes are built from controlled vocabulary gained from published ontologies (Ontology Lookup Service. Controlled vocabulary and schemes are stored in a database that also manages the access of the user to the web tool. From the webpage, schemes are downloaded as XML-files, which can be transferred easily to the memory of the PDA or exchanged between users. On the terminal, the GUI displays the schemes and stores data in csv and xml format. After manual quality control, data are uploaded via a webpage to an independently hosted results database, in which data are stored in an entity-value structure to provide maximum flexibility. Datasets are linked to the data file, which is stored on a file server. During upload, datasets receive an ownership stamp based on the name of the user performing the upload, a project affiliation and a date stamp. The information is used to regulate access to the data on the access webpage, which permits download of data belonging to the user or to the user’s projects, or to data for which the embargo period has ended. Together with a longterm data storage facility, the system provides a well-structured, but flexible data acquisition and management structure to ensure longterm accessibility of raw data. The longterm viability of the system critically depends on a sufficiently large, self-supporting user community. The growth of this community was hampered, partially because Windows, for which the system was implemented, was outrun by iOS and Android as a mobile device system. Furthermore, the decision, to use a more complex but well organised data management system requires more support from the project leader site. A third obstacle for central data management is a substantial fear of many researcher that centrally stored data may be misused, especially as they do not seem to be protected by copy right. Here, some political and legal issues linked to open access of raw data remain to be solved.
Publications
- A tool for phenotyping based on mobile terminals.‐ technical details. Phenodays Wageningen Sep 2012
Gremmels, J Köhl, K
- A tool for rapid phenotyping and standardized data storage including meta‐information. Phenodays Vaalsbroek Oct 2013
Köhl, K., Gremmels, J.
- Tools to catch (meta) data for phenotyping. Crop.Sense Symposium, Bonn, Sep 2014
Gremmels J, Basler G, Köhl, KI
