• Rough draft

    • 2.a Automate export from your local system

    Owned by Kees Burger
    Last updated: Aug 02, 2024 by Lucie Kulhankova
    2 min read

    Introduction

    If your local system doesn’t support the feature to directly expose metadata, you can use the following approach as an alternative. Instead of utilizing the 1.a Expose your local system approach, this method involves conducting automated exports from your institute’s local system through a script or workflow. By doing so, the export logic is moved outside of the source application.

    This approach requires the knowledge of a data steward in collaboration with the local IT department.

    Explanation / Approach

    The data we want to export is stored within a specific application used within the institute. To automate the export process, we need to access the raw data that lies beneath this application. This can typically be done either by accessing the data through an API provided by the application, or by directly connecting to the database where the data is stored (read access). This allows us to retrieve the data automatically without manual intervention.

    Img2Catalog application

    An example application that allows automatic export from your local system to FAIR data point is img2catalog, a registration tool developed by Health-RI, which simplifies the registration of image datasets. This tool queries an XNAT instance and generates DCAT-AP 3.0 metadata.

    It can register image collections directly at Health-RI FAIR Data Point, as well as at a local FDP that can then be linked to the national health data catalog.

    For details regarding installation and use, see GitHub - Health-RI/img2catalog: Repository for a tool to help make XNAT into a FAIR Data Point

    Pros / Cons

    Pros

    • Automated exports of data reduce the need for manual entry. Manual input is more error-prone, more labor-intensive and less future-proof

    Cons

    • Requires technical expertise,

    • If the underlying data structure or API endpoints change, this may cause disruptions in the export script or workflow.

    Next steps

    If you have an FDP and compliant metadata (Metadata mapping ) within your FDP, the data can be harvested by the National Catalogue. For this step, please contact servicedesk@health-ri.nl .