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UseRestrictionGrammar.md

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Use Restriction Grammar

A Consent or Research Purpose is a rendering of an OWL class, into JSON, using the following grammar:

Consent := {
  "restriction": UseRestriction
}
 
ResearchPurpose := {
  "restriction": UseRestriction
}

A use restriction expression represents a consent attached to a single sample or collection of samples or a research purpose. The "restriction" field contains the structured use restriction.

UseRestriction := 
    OrExpression
  | AndExpression
  | NotExpression
  | NamedExpression
  | EverythingExpression
  | NothingExpression

OrExpression := { 
  "type": "or", 
  "operands": [ UseRestriction* ]
}

AndExpression := { 
  "type": "and", 
  "operands": [ UseRestriction* ]
}

NotExpression := { 
  "type": "not", 
  "operand": UseRestriction
}

NamedExpression := { 
  "type": "named", 
  "name": <string>
}

EverythingExpression := { 
  "type": "everything"
}

NothingExpression := { 
  "type": "nothing"
}

Common Examples

Named Conditions

Intermediate forms of use restriction are usually represented using the NamedExpression and the boolean operators (And, Or, Not). For example, a sample which was only available for use in cancer research might be annotated with the expression:

// Consent restriction only for Cancer
{
  "restriction": {
    "type": "named",
    "name": "http://purl.obolibrary.org/obo/DOID_162"
  }
}

Or Conditions

If a study were restricted to cancer (DOID:162) OR heart disease (DOID:114), we could represent that with the following expression:

// Consent restriction for Cancer OR Heart Disease
{
  "restriction": {
    "type": "or",
    "operands": [ 
      {
        "type": "named",
        "name": "http://purl.obolibrary.org/obo/DOID_162"
      },
      {
        "type": "named",
        "name": "http://purl.obolibrary.org/obo/DOID_114"
      }
    ]
  }
}

And Conditions

And conditions typically incorporate different categories of information. Studies that restrict data usage only to research for pediatric cancer are a good example of that. Such an expression might be expressed this way:

// Consent restriction for Pediatric Cancer
{
  "restriction": {
    "type": "and",
    "operands": [ 
      {
        "type": "named",
        "name": "http://purl.obolibrary.org/obo/DOID_162"
      },
      {
        "type": "named",
        "name": "http://www.broadinstitute.org/ontologies/DUOS/pediatric"
      }
    ]
  }
}