Metadata for EJP rare disease patient registries, biobanks and catalogs

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

EJPRD namespace nomenclature

• The scheme : https
• The authority: https://www.ejprarediseases.org/
• The path : "/"
• The fragment: starts with "#"
• For defining ejprd vocabulary : https://www.ejprarediseases.org/metdata/core
• For defining the ejprd classes: https://www.ejprarediseases.org/metadata/core#ClassesA
• For defining the ejprd properties: https://www.ejprarediseases.org/metadata/core#PropertiesA

WORKFLOW FOR EJP-RD METADATA PUBLISHING

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.

Validators:

• 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:

Metadata core schema for VP

EJP-RD Catalog schema blocks

• The EJP-RD VP Catalog Schema in JSON format

  • The Catalog Entity here
  • The Catalog-Patient-Registry here
  • The Catalog-BioBank here
  • The StudyDesign here
  • The Biological-Sample here
  • The Biological-Sample-Patient here
  • The Organisation here
  • The Date-Time here
  • The Property-Value here
  • The Location here
  • The EUPID here
  • The Code here
  • The Coding-System here

  EJP-RD Data format converter (JSON to RDF) workflow

  

• The Validators - ShEx Constrains Schemas

  • The ShExC for Catalog-BioBank here
  • The ShExC for Catalog here
  • The ShExC for Catalog-PatientRegistry here
  • The ShExC for EJP-RD Metadata Core here

• 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 "