upload_config.yaml

generic_list:
  study_oid: S_PROTRAIT
  study_identifier: ProTRAIT - Generic
  event_oid: SE_GENERIC
  form_oid: F_PROTRAIT_GEN_2
  item_group_oid: IG_PROTR_GEN
  identifier_colname: GEN_IDNUMBER
  birthdate_colname: GEN_YEAR_BIRTH
  birthdate_isyear: TRUE
  gender_colname: GEN_GENDER
  item_prefix: I_PROTR_
  query: |
    prefix rr: <http://www.w3.org/ns/r2rml#>
    prefix ex: <http://example.com/ns#>
    prefix map: <http://mapping.local/>
    prefix sty: <http://purl.bioontology.org/ontology/STY/>
    prefix sio: <http://semanticscience.org/resource/SIO_>
    prefix foaf: <http://xmlns.com/foaf/0.1/>
    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 roo: <http://www.cancerdata.org/roo/>
    prefix icd: <http://purl.bioontology.org/ontology/ICD10/>
    prefix skos: <http://www.w3.org/2008/05/skos#>
    prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
    prefix uo: <http://purl.obolibrary.org/obo/UO_>
    prefix time: <http://www.w3.org/2006/time#>

    SELECT DISTINCT
    ?GEN_IDNUMBER
    ?GEN_GENDER
    ?GEN_AGE
    ?GEN_TREAT_CENTRE
    ?GEN_PLAN_COMPARISON
    ?GEN_YEAR_BIRTH

    WHERE {
     
      ?Patient rdf:type ncit:C16960;
   
      roo:is_born ?bYear.
      ?bYear roo:P100027 ?GEN_YEAR_BIRTH. 

      OPTIONAL{
      ?Patient rdf:type ncit:C16960;
      roo:P100061 ?id.
      ?id roo:P100042 ?GEN_IDNUMBER.
      ?Patient roo:P100018 ?gender.
      ?gender roo:P100042 ?GenderValue.

      BIND(
      COALESCE(
      IF (?GenderValue = "V ", "f", 1/0),
      IF (?GenderValue = "M ", "m", 1/0),
      "9" )
      AS ?GEN_GENDER)
      }

      OPTIONAL{
      ?Patient roo:P100016 ?age.
      ?age roo:P100042 ?GEN_AGE.
      FILTER (?GEN_AGE !=0)
      FILTER (?GEN_AGE !=1)
      FILTER (?GEN_AGE !=2)
      FILTER (?GEN_AGE !=3)
      FILTER (?GEN_AGE !=4)
      FILTER (?GEN_AGE !=5)
      FILTER (?GEN_AGE !=6)
      FILTER (?GEN_AGE !=7)
      FILTER (?GEN_AGE !=8)
      FILTER (?GEN_AGE !=9)
      FILTER (?GEN_AGE !=10)
      FILTER (?GEN_AGE !=11)
      FILTER (?GEN_AGE !=12)
      FILTER (?GEN_AGE !=13)
      FILTER (?GEN_AGE !=14)
      FILTER (?GEN_AGE !=15)
      FILTER (?GEN_AGE !=16)
      FILTER (?GEN_AGE !=17)
      FILTER (?GEN_AGE !=18)

        
    }

    OPTIONAL{
    ?Patient roo:P100039 ?treatingCentre.
    ?treatingCentre roo:local_value ?treatCentreValue.  } 
     
    BIND(
    COALESCE(
    IF (?treatCentreValue = "Maastro Clinic", "3", 1/0),
    IF (?treatCentreValue = "met name cochlea rechts van 14.4 naar 38.4 Gy (acceptabel) en brain Dmax van 46.6 naar 60.1 Gy (acceptabel)", "3", 1/0),
    IF (?treatCentreValue = "null", "0", 1/0),
    "9" )
    AS ?GEN_TREAT_CENTRE)

    OPTIONAL{
    ?Patient roo:P100024 ?radiotherapy.
    ?radiotherapy roo:has_planning_comparison ?plancomp. 
    ?plancomp roo:P100042 ?genplancomp.
    ?genplancomp roo:local_value ?GEN_PLAN_COMP1.}
     
    OPTIONAL{  
    ?Patient roo:P100024 ?radiotherapy.
    ?radiotherapy roo:has_planning_comparison ?plancomp.         
    ?plancomp roo:P100228 ?plancompdate.
    ?plancompdate roo:P100042 ?GEN_PLAN_COMP_DATE.}
         
    BIND(BOUND(?GEN_PLAN_COMP_DATE) as ?GEN_PLAN_COMPARISON)  
     
    BIND(
    COALESCE(
    IF (?GEN_PLAN_COMPARISON = true, "1", 1/0),
    IF (?GEN_PLAN_COMPARISON = false, "0", 1/0),
    "9" )
    AS ?GEN_PLAN_COMPARISON)
     
    }