SPARQL right-censored to binary

right-censored-to-binary.sparql

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
prefix snomedct: <http://purl.bioontology.org/ontology/SNOMEDCT/>
prefix roo: <http://www.cancerdata.org/roo/>

INSERT {
    GRAPH <http://inferred-manually.local/> {
    	?patient roo:survival_5_years ?survival_5y.
    }
}
where {
	?patient rdf:type snomedct:116154003;
          roo:P100028 [
        	roo:P100042 ?vital_status_value
          ];
    	  roo:P100008 [
        	roo:P100311 [
        		rdf:type snomedct:445320007;
        		roo:P100042 ?vital_status_days;
          ];
    ].
    
    # Determine the time interval to make binary
    BIND( xsd:boolean(IF(?vital_status_days > 1825, "true", "false")) AS ?gt_5y).
    
    # Make the outcome (survival) binary
    BIND( xsd:boolean(IF(?vital_status_value = xsd:integer("0"), "true", "false")) AS ?survived).
    
    # In the case when survival is less than time interval, AND survival true we need to make this unknown.
    # In all other situations we can make the bind (hence testing the exemption case and the negation to make the bind in the end)
    OPTIONAL {
        FILTER ( !( (?gt_5y = xsd:boolean("false")) && (?survived = xsd:boolean("true")) ) )
        BIND( xsd:boolean(IF(?survived && ?gt_5y, "true", "false")) AS ?survival_5y).
    }
}