what is local system that export metadata( EPD, local data management system, Molgenis, Beacon? XNAT (health ri repository, img2catalog)
Introduction
The option to expose your metadata from an institute local system, available in your institute, allows for the closest link between the source data and the public metadata. The responsibility for maintaining the Enabling your institute's local system to directly expose metadata creates the strongest connection between your original data and publicly available information. This setup means that responsibility for maintaining this metadata is kept at the source, be it whether handled by software or people. This approach Achieving this requires either a system that already incorporates supporting this behaviour, feature or deep knowledge of the source system and the availability of software engineering capacity to extend the functionality of the system.
When considering sharing your data with the public, think about using local systems like local data management systems, Molgenis, or XNAT. These systems establish a direct pathway between your original data and public information, ensuring that you're in charge of managing your data within your institute.
Explanation
The platforms/systems used To facilitate this process, ensure that the systems in your institute should allow extensions to expose the metadata of existing source data. If the system is closed or the vendor is not able to add this behaviour, an alternative approach could be the support extensions for displaying metadata from your existing data sources. If your system lacks this capability, you canhttps://health-ri.atlassian.net/wiki/spaces/FSD/pages/edit-v2/292519963?draftShareId=3e2fb8f1-0cba-4f12-a724-d664f2b9bf2c as an alternative.
MOLGENIS implementation of the FDP extension.
MOLGENIS partly supports the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles. FDP is implemented in MOLGENIS EMX2 in compliance principles, including the FAIR Data Point (FDP) extension. The FDP implementation within MOLGENIS EMX2 complies with the latest v1.1 specification of the FAIR Data Point available at specs.fairdatapoint.org.
Setup and configuration
The easiest way to enable FDP in MOLGENIS EMX2 is by choosing ‘FAIR_DATA_HUB’ as a template for your database. This will add three tables that will define the content of your FAIR Data Point: Catalog, Dataset and Distribution. Loading the ‘FAIR_DATA_HUB’ template including the example data will result in a fully operational FAIR Data Point. The example data can be used as a reference on how to enter data into the system. It can be safely removed or replaced.
Before the FDP can be used, log in as the admin user and visit your FDP at <server>/api/fdp. This will add a database setting called FAIR Data Point root metadata to the schema that enables your FDP. This setting contains a piece of RDF/TTL that is part of your FDP root endpoint which is fully customizable. Here, you can change the information about your FDP such as title, publisher, contact point and language. To make changes, go to your FDP-enabling schema, go to Settings, Advanced settings, and click the Edit button for FAIR Data Point root metadata.
After setting up these tables, this is how its contents are translated to the FDP structure:
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Each Dataset contains a reference to one or multiple Catalogs via the belongsToCatalog field.
These references can also be viewed in the referred-to Catalogs via the
datasetfield.
Each Distribution contains a reference to one or multiple Datasets via the belongsToDataset field.
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. This means that MOLGENIS allows you to establish a connection with a FAIR Data Point. For setup and configuration instructions, please refer to the https://molgenis.github.io/molgenis-emx2/#/molgenis/dev_fairdatapoint?id=fair-data-point.
Usage example
MOLGENIS offers extensive customization options and the ability to develop applications, as demonstrated by the BBMRI-ERIC project.
Using the MOLGENIS framework, the team implemented catalogue software to automatically generate tailored FAIR catalogues and web applications based on a custom-defined data model. This included creating query user interfaces, a main menu, questionnaire/survey forms, and tools for data curation.
The implementation process began with conceptualizing the data bank/data source, informed by extensive interviews and analysis. Background knowledge from previous cataloguing efforts, such as H2020 projects like LifeCycle and EUCAN-connect, was also incorporated. The results were translated into a structured data model in MOLGENIS, followed by prototyping activities to refine user interfaces.
The UMCG received contributions from the EUCAN-connect project, ensuring open-source development and promoting long-term sustainability and interoperability. Further details can be found in MOLGENIS manuals and scientific publications.
XNAT img2catalog
XNAT img2catalog is a tool that extracts metadata from XNAT instances and generates DCAT-AP 3.0 metadata. Each XNAT project is treated as a separate dataset. While this tool lacks features for updating existing datasets, it provides a means to connect your data with a FAIR Data Point. However, it's important to note that the tool currently does not fully utilize all aspects of FAIR data principles, such as updating existing datasets and setting language for fields.
You can find more information and instructions on installation and usage here: https://github.com/Health-RI/img2catalog.
pros/cons
Pro
Responsibility of maintenance lies closest to the owner(s) of the source material
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