NFDI4Biodiversity Use Case
The NFDI4Biodiversity project aims to integrate and enhance the accessibility of biodiversity data, specifically focusing on the plant genetic resources (PGR) held by the IPK (Leibniz Institute of Plant Genetics and Crop Plant Research). The main objectives include:
Integration into Research Data Commons (RDC): The project seeks to incorporate the biodiversity data from IPK's PGR into the RDC, facilitating easier analysis and networking of this valuable data.
Development of User-Friendly Tools: A key goal is to enable researchers to access and utilize tools that assist in the analysis of genotypic and phenotypic data. This includes creating web applications and workflows that support:
Focus on Crop Diversity: While primarily concentrating on major crops such as wheat, barley, oats, and beans, the tools and workflows developed are designed to be applicable to a wider range of species, thus benefiting the broader biodiversity community.
Standardization of Data: The project emphasizes the importance of standardizing phenotypic data through the MIAPPE standard, which helps researchers organize and process data effectively. The development of the MIAPPE Wizard allows users to create required information in MIAPPE format easily.
Enhancing Interoperability: By working on the advancement of BrAPI, an interface for interoperability between plant breeding databases, the project aims to streamline data access and exchange among various platforms.
Through ongoing collaborative efforts, several promising findings have emerged:
Successful Integration of Data: Initial pilot projects, such as MIRA, have demonstrated the feasibility of providing phenotypic data structured according to the MIAPPE standard. This pilot illustrates the potential for effective data integration within the RDC.
Enhanced Accessibility: The development and implementation of web applications and workflows have simplified access to complex genotypic and phenotypic analyses, allowing researchers to conduct more sophisticated studies with ease.
Standardization Impact: The MIAPPE Wizard has proven to be a valuable tool for researchers, enabling efficient data organization and compliance with the MIAPPE standard, which enhances data usability and sharing.
Interoperability Potential: The ongoing development of BrAPI has shown promise in connecting various tools and databases, facilitating a more integrated approach to plant breeding and biodiversity research.
Overall, the NFDI4Biodiversity project is making significant strides toward enhancing the organization, accessibility, and usability of biodiversity data, ultimately supporting more effective research and collaboration within the scientific community.
This API server allows researchers to submit phenotyping observations to a dataset stored as an Annotated Research Context (ARC). The ARC provides a standardized structure for capturing and sharing research data, enabling reproducibility and transparency in scientific investigations.
DivAssociate is a workflow implemented in Nextflow to perform a GWAS using GEMMA's Linear Mixed Model algorithm. It uses genotyping data in VCF format and phenotyping data in a CSV file.
DivPortal is a web app that visualizes and explores plant phenotyping trials. It uses a BrAPI server for the data backend and to visualize results and germplasm information. It also integrates a brokering service for analysis workflows between workflow managers and the connected BrAPI server.
GridScore is a field trial phenotyping app for trait data. It lets you keep track of what's happening in the field on a plot-level basis. This could be anything from plant emergence, flowering date, plant height, flower colour, etc.
User-friendly application for creating FAIR- and ISA-compliant metadata for results of life science experiments.
Enabling Access to MIAPPE-compliant ISA Tab archives through BrAPI