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How to turn Define into a JSON-LD context

Add 'what is this thing' to datasets with a single "@context" line

Convert Define-XML into JSON using the Define-XML schema

const convert = require(`${module.path}/src/utils/convert.js`)
convert.xmlToJson(
    xmlPath,
    xmlPath.split('/').pop().replace('.xml','.json'), 
    `${module.path}/mappings/define2_1_0.js`)

Map the types to JSON-LD

To do this we need to create a context that adds "@type" and "@id" to all structures

The JSON unmarshaller helpfully maps all XML types to TYPE_NAME so JSON-LD can interpret these as types via a single line within the JSON-LD @context

"TYPE_NAME": "@type"

Turn the ODM objects into nodes in the JSON-LD Graph by identifying them

ID can be obtained by the ODM OID e.g.

"oid": "@id"

By flagging the appropriate identifiers in the Define as "@id" type, the objects become accessible via these IDs in JSON-LD form.

For example applying this context

"oid": "@id",
"itemGroupDef": {
        "@container": ["@id", "@set"],
        "@id": "def:define2_1_0.ODMcomplexTypeDefinitionItemGroupDef"
}

to the Define data

"itemGroupDef": [  
        {
        "TYPE_NAME": "define2_1_0.ODMcomplexTypeDefinitionItemGroupDef",
        "oid": "IG.ADADAS",
        "name": "ADADAS",
        "repeating": "Yes",
        "isReferenceData": "No",

results in a node that can be dereferenced by its identifier when the expanded JSON-LD is re-compacted/framed, as seen here

 "itemGroupDef": {
    "IG.ADADAS": [
      {
        "isReferenceData": "No",
        "purpose": "Analysis",
        "repeating": "Yes",
  ...

Map CDISC ODM to JSON-LD for internationalisation in web-based applications

This is based on the JSON-LD documentation and needs testing

"lang": "@language",

"translatedText": {
        "@container": "@language",
        "@id": "schema:PropertyValue"
}

** MORE WORK NEEDS TO BE DONE **

  • At time of writing, the transformation to JSON and then JSON-LD has facilitated an easy-to-access Define JS object
  • Define graph still needs to be made, and then combined with dataset graph
  • Testing and proof of concept for internationalisation is needed
  • Value-level metadata support needs adding
  • Slicing (RDF data cubes) support needs adding
  • Biomedical concept support needs adding