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Introduction

Metadata

All the research produced in the CropXR consortium will be well annotated with metadata following the CropXR standards.

The metadata annotation will have multiple uses:

  • Findability of your study, by other researchers in the consortium
  • Reusability of your data by other users in the consortium
  • Improvement of your own data annotation

The responsibility to annotate the data lies with the researcher, with the help and tools provided by DataXR.

CropXR uses established standards for metadata on plant research, combining elements from:

  • ISA (Investigation-Study-Assay) framework for structuring research data
  • MIAPPE (Minimum Information About Plant Phenotyping Experiments) for phenotyping studies
  • ENA (European Nucleotide Archive) standards for sequencing data

Model flexibility

A standardized metadata format ensures that the metadata has a predictable structure. There are however many different types of studies in the consortium, with different metadata that is important. To fit all different studies in the same format there is a certain flexibility in the model.

This means you need to understand the model well and decide how to apply it to your study. These documents should provide the information needed to make those choices. For the first time entering metadata, plan sufficient time to understand the model.

If you are stuck at any point, things are unclear, or you need help, please reach out to the DataXR team at data@cropxr.org

Catalogue

Metadata is now collected in the Catalogue website. In this catalogue people of the consortium can find studies, view and download the metadata, and view the associated data. The researchers who produced the data decide who can view their study. Detailed instructions on how to fill in metadata can be found here.

If you have already filled in the Excel templates, or have started filling them in, contact the DataXR team at data@cropxr.org. The team will help you enter your metadata into the catalogue.

Data

Data is stored in the Resilience Hub, together with the metadata in the catalogue. Each dataset is linked to an assay in the catalogue, so others can see what experiment the data comes from. Who can download a dataset follows the sharing settings of the study in the catalogue.

Data is uploaded and downloaded with the command line tool:

  • Uploading: enter your metadata in the catalogue first, then upload a folder of data to the matching assay.
  • Downloading: find the dataset in the catalogue and use its identifier to download it.

Research Drive

Data was previously stored on Research Drive. It is no longer used for new studies, but existing data remains available there for now.