General Workflow

Preparations

1. Understand the basic structure of the metadata model.
2. Decide what experiments to group into the study.
3. Choose the study type (sequencing, phenotyping or combined). Inform DataXR well up front when your study does not fit these types.
4. Gather the files with the metadata that you already collected. This includes e-lab journal entries, files that outline experimental conditions per plant, files that link output files to the experiment, etc.
5. Make a plan of what data should be uploaded and how it should be organised into datasets. Each dataset is uploaded as one folder and belongs to one assay.

No separate registration step

There is no separate registration form. All metadata goes into the data catalogue, and that is where you register your investigation and study.

Minimal metadata entry

Decide how to group conditions and samples, so that all the information you need is captured. In the catalogue, fill in all the fields that are essential to understand the study, focusing on key aspects, such as species and assay type. Make sure every assay you want to upload data to exists, so others can find and understand your data.

Data upload

Your metadata has to be in the catalogue before you can upload, because each dataset is uploaded to an assay.

Pre-requisites:

• Install the command line tool rhub and sign in. You do this once.
• Check that you have access to the assay you are uploading to, and know its assay id.

Steps:

1. Put everything that belongs to a dataset into one folder.
2. Upload the folder to the matching assay with rhub upload.
3. Your work package lead approves the upload, after which the dataset appears in the catalogue.

Research Drive

Uploads to Research Drive are no longer possible for new studies.

Improving metadata

At any point in time you can save the metadata and edit it later. Add any additional metadata you collected; this makes your data easier to reuse.

Other things

Adding columns

You can add columns for relevant metadata that the provided columns do not cover. Before you do, please ask an expert to check that the information is not already covered by an existing column.

Combined study

For instructions on the metadata of a combined study, read here.

Ontology lookup

Ontology terms make metadata much clearer, but finding the right term across different ontologies can be difficult and time consuming. We are still working on improving the workflow for researchers and are open to suggestions.

If the suggested sources for ontologies do not cover the exact conditions, and you think a specific term could be useful throughout the consortium, please contact us. It is likely that there will be a list of CropXR specific terms, that can be referenced.