This is for publishing European Joint Programme (EJP) for Rare Disease virtual platform metadata for Biobanks and Catalogs metadata, through the extraction, conversion, RDF schema and validating the data RDF data using the ShExC.
We are also working to align with similar schema standardisation efforts such as RD connect semantic model, schema.org, bioschemas, MIABIS and GA4GH (see also schema blocks and phenopackets. A proposed semantic model for the Common Data Elements can be found here.
This diagram illustrates the basic idea of the metadata publication workflow. Components are independent and can be used and new blocks can be defined that inherit from parent blocks.
For more details on the metadata see the WIKI page
This is the entire codebase for the EJP-RD Metadata publishers. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements from the rare disease community and other more generalised standards for data sharing such as the W3C DCAT vocabulary.
EJP-RD Metadata standard is build around two major standards - JSON and RDF standard models for data exchange.
JSON Schema tool for validating the structure of JSON data, from the various registries, biobanks, or etc through the API or Web URL.
RDF schema tool for validating the RDF graph
ShEx Schema tool for validating the RDF graph data
The metadata core schema as shown for the EJP_RD virtual platform(VP) displayed below:
The EJP-RD VP Catalog Schema in JSON format
The Validators - ShEx Constrains Schemas
The JSON to RDF converter here
The jar file can be invoke from the command line using the following command : " cat "filename".json | java -jar json2rdf.jar https://www.ejprarediseases.org/metadata# | riot --formatted=TURTLE "