Metadata for EJP rare disease registries, biobanks and catalogs

As part of the European Joint Programme (EJP) for Rare Disease, we are developing common schemas for rare disease resources to expose metadata to the EJP virtual platform (VP). The schemas are expressed as a number of schema blocks that can be combined to create rich metadata objects. The schema blocks will be published as JSON schem modules with a semantic mapping to standard vocabularies using JSON-LD.

The core model is designed to represent data about a rare disease resource, these include rare disease registries, biobanks, expert networks and catalogs of resources. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements initiatives in the rare diesease community and other more generalised initiatives such as the W3C DCAT vocabulary. We are also working to align with similar schema standarisation 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.

Status: DRAFT - 1st May, 2019. This is currently a strawman proposal intended to generate discussion and help in developing an early demonstrator.

Schema block elements overview

This diagram illustrates the basic idea of a schema block. Blocks are reusable components and new blocks can be defined that inherit from parent blocks.

Resource level JSON schema

A example of a catalog block in JSON schema is described in catalog_block.json.

A simplified representation of the same data in CSV format is in catalog_block.csv.

Example data

An example instance of a resource level metadata taken from Orphanet can be seen in orphanet_24435.json.

{
  "@id":"https://www.orpha.net",
  "@type": "Catalog",
  "name": "Orphanet catalog of registries",
  "homepage": "https://www.orpha.net"
}

{
  "@id":"24435",
  "type": "PatientRegistry",
  "name": "Selbsthilfegruppe Ektodermale Dysplasie",
  "description": "Die Ektodermale Dysplasie (ed) ist eine genetisch bedingte Erkrankung. Typisch für uns ist, dass wir nicht, oder nur wenig schwitzen können, dass Zahnanomalien auftreten, Zähne fehlen oder in spitzer Form wachsen, dass Kinder Flaumhaare haben und der Haarwuchs weniger als normal ist. Eine genaue Beschreibung der Symptome und der Ursachen können Sie in der Rubrik „Was ist ed“ nachlesen.",
  "theme": [ { "id" : "Orphanet:398189"} ],
  "homepage": "http://www.ektodermale-dysplasie.de",
  "location": { "country" : "Austria" },
  "inCatalog" : [ {  "@id":"https://www.orpha.net" } ]
}

RDF + JSON-LD

You can apply the JSON-LD context from ejp_vocabulary.jsonld to any JSON document to generate an RDF representation. An example of a resource entry in RDF turtle format is in orphanet_24435.ttl

Schema.org

The schema blocks are designed to be compatible with schema.org style markup that allows you embedd the metadata into Web pages. Both RDFa and JSON-LD representations are supported microformats. See an example of a draft schema.org proposal for a patient registry.

Use cases

• Provide minimal metadata to describe a rare disease registry or biobank, or a catalog of registries or biobanks. The metadata should be sufficent to expose data aboutthese resource through the virtual platform
• Provide a uniform way for resources to expose the primary disease using a Orphanet code so that resources can be searched by disease in the virtual platform
• Provide a mechanism to identify resources and harmonise duplicate resources across catalogs
• Provide geographical infomation so resources can be filtered by country in the VP
• Expose if resources contain data about individuals with a rare disease e.g. a patient registry
• Expose if resources provide metrics about individuals, such as number of cases
• Expose if a resource has access to biological samples, such as tissue or cell ines.
• Expose if the resource has further contact information
• ...