A. Annex: Data transfer checklist
This section summarises in a comprehensive table all the actions to be performed in the case of Data Holders that will upload their data into a reference node.
Initial Assessment
Submit an application for data incorporation use cases
Complete the application for data incorporation use cases form for the Access Committee to evaluate the scientific relevance of your participation in EUCAIM as a data holder.
Complete the TIERs maturity level questionnaire
Complete it to assess the readiness and compliance of your datasets and categorize them according to their maturity level (TIER 1, 2, or 3).
Complete the DW maturity level questionnaire (only for clinical sites, as hospitals)
Complete it to determine the current state of the hospital's Data Warehouse preparedness and maturity.
Ethical and Legal
Provide documentation
Proof of legal representation and legal basis if necessary.
A copy of a favorable ethical approval (if applicable).
A report from the DPO confirming legal compliance.
Any documents required under your national legislation
Terms of Usage for the data.
D4.4 Final rules for participation report (See Sections 4.4.1 (Legal requirements) and 4.4.2 (Ethical requirements for Data Holders)
Preliminaries
Get Familiar with EUCAIM
Follow the EUCAIM training material and brief documents.
Browse architecture and
Watch webinars and videos.
Request a EUCAIM User
Request a EUCAIM User in the Dashboard through LS-AAI.
Data Preparation
Extract Imaging and clinical data
Use your own tools to extract the Medical Images and the clinical data
N/A
Annotate the data (optional)
Use your own annotation tool or the one selected by EUCAIM (MITK). Convert the annotations into DICOM-SEG.
Data de-identification
Ensure that no identifiable information is present in the dataset. If your imaging data are not already de-identified, you may use the Lethe DICOM Anonymizer-
Re-identification risk assessment (optional)
Assess the risk of re-identification of patients based on your imaging metadata by checking hidden DICOM Tags.
- Wizard
Data Quality Assessment (optional)
You may check the accuracy and integrity of your imaging dataset
Data Uploading
Provide Data Ingester Account Details
Open a ticket in the helpdesk, select the "Reference nodes" group (or "Technical support team" if unavailable) and add a request with the title: "Create a data ingestion project in UPV" or "Create XNAT project in HealthRI" (depending on the Reference site), providing the name of the project, the username in EUCAIM who will manage it. An answer will be given soon.
Download and install the Data Ingestion tool
Download the Data Ingestion tool for the UPV node and the Clinical Trial Processor (CTP) for HealthRI
Request a user in the Reference node
Choose the reference node where the data will be uploaded (only one):
UPV (login button, register through LS-AAI and ask for a "Data Ingester" account)
Upload Imaging Data
Upload imaging data in the platform as described in the instructions (6.2.2 for UPV node and 6.2.3 for Health-RI).
Upload clinical Data
Once medical imaging data is uploaded, you can proceed with the clinical data. If the process of converting the clinical data is expected to be long, we encourage you to create an “image-only” dataset by skipping this step. Use the same tool as before for UPV and XNATpy for Health-RI. Data can be in CSV or JSON.
Dataset Creation
Create and Publish the Dataset
The dataset has to be created according to the instructions in the Gitbook (section 6.2.2.3 for UPV and 6.2.3 for Health-RI).
Provide the dataset's metadata
Provide the metadata of the datasets according to the EUCAIM schema. In case of doubts with the terminology, use textual descriptions.
Make a request of registry upload
Create a helpdesk ticket on the category catalogue, providing the spreadsheet file with the metadata information. The helpdesk team will contact you back informing if the dataset has been properly registered or requesting more information.
Verify the entries in the catalogue
Access the registry in the catalogue and verify the collection.
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