General Workflow

Preparations

1. Understand the basic structure of the metadata model.
2. Decide on the 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. Make sure that you have registered your study in this form. After the admin has checked the registration, you will receive a study id you need when entering the metadata, as well as storage for your experimental data.
5. 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.

Data Upload

Pre-requisites:

• access to the Research Drive
• Choose a method of data upload, depending on your data size, and set up the required tools.

Steps:

1. Make a plan of what data should be uploaded and how it should be organised in folders.
2. Upload the data inside your designated study folder.

Minimal metadata entry

Decide how to the metadata should be entered, to capture all information that is needed, by grouping conditions and samples. In the web interface, fill in all the fields that are essential to understand the study, focusing on key aspects, such as species and assay type. In this phase you also link the data to the performed experiments, so others can find and understand your data.

Improving metadata

At any point in time you can save the metadata and edit it later. Add the additional metadata that was collected, and improves the re-usability of your data.

Other things

Adding columns

It is possible to add additional columns to capture metadata relevant, not in the provided columns. Before doing this, please consult an expert of this is not already covered by the existing columns.

Combined study

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

Ontology lookup

Annotation with ontology terms can greatly improve the clarity of metadata, but finding the right term, spread out over different ontology systems can be challenging 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.