Extending Tripal for Community-Based Management and Distribution of Genotypic and Phenotypic Data

Tripal is a freely available, open-source construction toolkit for community-focused, biological data web portals. There is a growing need for community-accessible storage of minimally filtered genotypic and phenotypic data collected by multiple research groups with the goal of increasing collaboration. In an effort to satisfy this need, we have developed two Tripal Extension modules (ND Genotypes, https://github.com/UofS-Pulse-Binfo/nd_genotypes; Raw Phenotypes, https://github.com/UofS-Pulse-Binfo/rawphenotypes) with tools to load, manage and distribute genotypic and phenotypic data. ND Genotypes provides an administrator-friendly interface which loads genotypes from multiple file formats efficiently; whereas, Raw Phenotypes provides a completely automated researcher-friendly upload page with Microsoft Excel file drag-and-drop upload, data validation and new trait detection. Genotypic data is presented to the user through a researcher-filtered marker-by-germplasm table in addition to being summarized on marker pages. Phenotypic data is summarized using a general heatmap diagram and trait-specific histograms. Both modules provide access-controlled download forms with filter and format options catering to further analysis of these data. These modules are currently in use on KnowPulse (http://knowpulse.usask.ca) and have been tested on a generic Tripal install to ensure they can be used by the wider Tripal community. In conclusion, these modules provide upload, visualization and download of minimally filtered and analyzed genotypic and phenotypic data within a Tripal community data web portal to ensure data is community-accessible for increased collaboration.