ExampleTurtlePairedReportsMay2010

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# Template for N3 document

# Allows use of unprefixed names instead of :name style names
# @prefix : <#>.
# #
# @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
# @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
# @prefix skos: <http://www.w3.org/2004/02/skos/core#>.
# @prefix owl: <http://www.w3.org/2002/07/owl#>.
# @prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
# @prefix dc: <http://http://purl.org/dc/terms/>.
# @prefix foaf: <http://xmlns.com/foaf/0.1/>.
# @prefix vcard: <http://www.w3.org/2006/vcard/ns#>.

@prefix term: <term:/> .
@prefix units: <units:/> .
#  @prefix : <tag:eric@w3.org:2009/tmo/translator#> .
  @prefix foaf: <http://xmlns.com/foaf/0.1/> .
  @prefix trans: <tag:eric@w3.org:2009/tmo/translator#> .  
  @prefix indivo: <http://indivo.org/vocab/xml/documents#> .
  @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  @prefix cpr: <http://purl.org/cpr/0.75#> .
  @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  @prefix ro: <http://www.obofoundry.org/ro/ro.owl#> .
  @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
  @prefix dct: <http://purl.org/dc/terms/> .

#
# Identify the document
# =====================================================================
# 12345678 - MM DIAGNOSTIC DIGITAL BILAT
# Patient: Mary Kay SMITH -- History #AB98765
# BILATERAL DIGITAL DIAGNOSTIC MAMMOGRAM POST LUMPECTOMY MAMMOGRAM:
# 1/1/2009
# CLINICAL: 611.72 Lump Or Mass In Breast-611.72 Patient with palpable
# abnormality in left breast. Post left lumpectomy. Recent MRI
# demonstrated suspicious lesions in left breast.
# ---------------------------------------------------------------------

# to make this more English-like, I give the document a name; "theDocument"

<> a cpr:patient-record .
  _:patient cpr:subjectOfDescription <> .

_:patient a cpr:patient ;
    cpr:patientID "AB98765" ;
    foaf:name "Mary Kay Smith" ;
    foaf:givenName "Mary Kay" ;
    foaf:familyName "Smith" ;
    trans:demographics [
        # indivo:dateOfBirth "??"^^xsd:date ;
        indivo:gender "Female" ]
    .

_:theRadiologist a trans:Radiologist ;
    foaf:name "Kenneth Kirk" ;
    foaf:givenName "Kenneth" ;
    foaf:familyName "Kirk" .

_:theClinic a trans:Practice ;
    trans:practiceName "Acme Hospital" .


_:patient trans:hasCondition [
    # cpr:startsNoLaterThan "2009-05-15T12:00:00"^^xsd:dateTime ;
    dct:label "LUMP OR MASS IN BREAST" ;
    trans:diagnosedWith term:BreastLump ;
    trans:ICD9 "410" ;
] .

_:patient trans:hasCondition [
    # cpr:startsNoLaterThan "2009-05-15T12:00:00"^^xsd:dateTime ;
    dct:label "palpable abnormality in left breast" ;
    trans:diagnosedWith term:Abnormality ;
    term:location [ a term:Breast ; term:laterality term:left ] ;  # @@new - inBodyOf?
    trans:ICD9 "@@" ;
] .

_:patient trans:procedure [
    # cpr:startsNoLaterThan "2009-05-15T12:00:00"^^xsd:dateTime ;
    dct:label "Post left lumpectomy" ;
    trans:codeProcedure term:CompletedLumpectomy ; # @@new
    term:location [ a term:Breast ; term:laterality term:left ] ;  # @@new
    trans:ICD9 "@@" ;
] .


[ a trans:Encounter ;
    trans:patient _:patient ;
    trans:physician _:theRadiologist ;
    trans:dateOfEncounter "2009-01-01"^^xsd:date ;
    trans:workingDiagnosis term:SuspiciousForMalignancy ;
    trans:reportedSymptoms "false" ;

    trans:test [
        a term:Mammogram ;
        indivo:dateMeasured "2009-01-01"^^xsd:date ;
        trans:testName "BILATERAL DIGITAL DIAGNOSTIC MAMMOGRAM POST LUMPECTOMY MAMMOGRAM" ;
        trans:result [
            a term:MammogramReport ;
            term:diagnosticCategory term:SuspiciousForMalignancy ;
	    term:ICD9 "611.72" ; # "Lump or mass in breast"
            dct:author [foaf:name "Jenny Jones"] ;
            trans:referredClinic _:theClinic ;
            term:finding [ # see theMassAt1 below
                rdfs:label "fine linear and pleomorphic calcifications" ;
		# @@ coded calcifications
                term:location [ a term:Breast ; term:laterality term:left ; term:position "1:00"^^units:clock];# new
		term:size [ term:x "3.1"^^units:cm ; term:y "3.1"^^units:cm ]
	    ] ;
            term:finding [ # not listed below
                rdfs:label "hypoechoic mass with related calcification" ;
                term:location [ a term:Breast ; term:laterality term:left ; term:position "2:00"^^units:clock];# new
		term:size [ term:x "8"^^units:cm ; term:y "8"^^units:cm ]
	    ] ;
            term:finding [ # see theMassAt9 below
                rdfs:label "spiculated margin" ;
                term:location [ a term:Breast ; term:laterality term:left ; term:position "9:00"^^units:clock];# new
		term:size [ term:x "1.2"^^units:cm ; term:y "1.3"^^units:cm ]
	    ]
        ]
    ] ;
] .

term:SuspiciousForMalignancy dct:identifier "Suspicious for Malignancy" .


[ a trans:Encounter ;
    trans:patient _:patient ;
    trans:physician _:theRadiologist ;
    # after trans:dateOfEncounter "2009-01-01"^^xsd:date ; ?
    trans:workingDiagnosis term:InvasiveAdenocarcinoma ;
    trans:workingDiagnosis term:DuctalCarcinoma ;
    trans:reportedSymptoms "false" ;

    trans:test [
        a term:Biopsy ;
        # after indivo:dateMeasured "2009-01-01"^^xsd:date ; ?
        trans:testName "ULTRASOUND GUIDED NEEDLE CORE BIOPSY" ;
        trans:result [
            a term:PathologyReport ;
            term:diagnosticCategory term:SuspiciousForMalignancy ;
	    term:ICD9 "611.72" ; # "Lump or mass in breast"
            # dc:author [foaf:name "John Madden"] ;
            trans:referredClinic _:theClinic ;
            term:finding [
                rdfs:label "DUCTAL CRIBRIFORM CARCINOMA IN SITU WITH MICROCALCIFICATIONS" ;
		# @@ coded calcifications "MICROCALCIFICATIONS: PRESENT IN ASSOCIATION WITH DCIS"
                term:location [ a term:Breast ; term:laterality term:left ; term:position "1:00"^^units:clock];# new
		term:scale [ term:nuclearGradeOfInSituCarcinoma "2"^^term:NuclearGradeOfInSituCarcinomaOF3 ] ;
	    ] ;
	    # hey, what happened to the 2:00 mass?
            term:finding [
                rdfs:label "INVASIVE DUCTAL ADENOCARCINOMA" ;
                term:location [ a term:Breast ; term:laterality term:left ; term:position "9:00"^^units:clock];# new
		term:scale [ term:nottinghamCombinedHistologicGrade "2"^^term:NottinghamCombinedHistologicGradeOF3 ] ;
		term:scale [ term:nuclearGradeOfInSituCarcinoma "2"^^term:NuclearGradeOfInSituCarcinomaOF3 ] ;
	    ]
        ]
    ] ;
] .

term:InvasiveAdenocarcinoma dct:identifier "Invasive Adenocarcinoma" .
term:DuctalCarcinoma dct:identifier "Ductal Carcinoma" .

# I haven't TMO-coded the following stuff from the N3 coding. - EGP 2011-05-10
#  <http://theHospital.example/2009/01/01/12345678>
#  
#  
#  theFinding-4 dc:label "Recent MRI demonstrated suspicious lesion in left breast"; = {thePatient :finding [a MRI; :result theMRIResult]}.
#  theMRIResult = {thePatient :finding [a Lesion; inBodyOf thePatient; :significance :Suspicious]}.
#  .
#  # the Description is best modeled using an "on-the-fly" vocabulary
#  aPriorMammomgram = [a MammogramReport; dated "2008-01-01"^^xsd:date; ].
#  aPriorBiopsy = [a UltrasoundBiopsyReport; dated "2007-01-01"^^xsd:date].
#  theDocument :part [= theDiagnosis; a Diagnosis; dc:author theRadiologist].
#  theRadiologist performs [a Comparison; between theDiagnosis, aPriorMammogram, aPriorBiopsy].
#  # or, theComparison is among (theDiagnosis, aPriorMammogram, aPriorBiopsy).
#  thePatient :has [a RightBreast; = theRightBreast], [a LeftBreast; = theLeftBreast].
#  bothBreasts = (theRightBreast, theLeftBreast).
#  	
#  # Now it gets really interesting
#  # do I model this as a finding, or as a fact?
#  # also, how many findings are there in the report? 1, 2, many?
#  # here I've modeled it as a single finding, which is shared by both breasts
#  theRightBreast :finding someFibroglandularElements.
#  theLeftBreast :finding someFibroglandularElements.
#  someFibroglandularElements = [a Finding; a [a owl:Restriction; owl:onProperty refersTo; owl:minCardinality 2]].
#  # this is an interesting statement, in that it uses a
#  someFibroglandularElements :qualifier scattered.
#  # or if you want to get fancy, you could say, "the finding is of >1 fibroglandular element", something like this:
#  
#  
#  
#  # here's more from the CSHALS:
#  
#  #  it's hard to imagine a medical document so elementary
#  
## that it wouldn't reference at least 
#  
## two (2) non-identical entities!
#  
#  

theMassAt9 a Mass.

#  theMassAt1 a Mass.

#  theMassAt9 owl:differentFrom	theMassAt1.
#  
theSpecimen contains theMassAt9, theMassAt1.
#  
#  # or, saving a line
# 
#  theSpecimen contains [a Mass; = theMassAt9].

#  
#  # theSpecimen contains [a Mass; = theMassAt1].
# 
#  theMassAt9 owl:differentFrom	theMassAt1.
#  
#  # in fact, you might want to collect all instances

#  # that you define and declare an owl:AllDifferent class
#  
# [a owl:AllDifferent]	 owl:distinctMembers
 (theRadiologist, thePatient, 
 theMassAt9, theMassAt1… ).
 

#  
#  
#  <http://theHospital.example/2009/01/01/12345678>
#      foaf:topic thePatient.
#  thePatient a Patient.
#  Patient a skos:Concept.
#  # later add whatever mapping axioms you want

#  # (we favor using SKOS whenever possible)...
#  Patient skos:broader foaf:Person;
 skos:closeMatch snomed:378243823, radlex:347439845,
 loinc:473878943.
#  
#  # or even add more forceful axioms

#  # (but beware of "ontological overcommitment")...
#  Patient rdfs:subClassOf dc:Agent;
 owl:equivalentClass gom:Patient.
#  
#  
#  # these are pretty commonplace assertion types

#  # hard to imagine much structural variation here

#  # can pick a specific vocabulary later
#  
#  # more sketchy, depends on chosen anatomy vocabulary

#  
#  # very sketchy
#  
# these are modeled loosey-goosey as value partitions
#  
# need no idea how e.g. Radlex might do this
#  
#  
theMassAt9 shape round.
#  
theMassAt9 margin indistinct.
#  
theMassAt9 echogenicity isoechoic.
#  
#  
#  # I (radiologist) am suspicious for malignancy.
#  theRadiologist suspects [a Malignancy].
#  
#  # This mammogram is suspicious for malignancy.
#  {theMammogram shows [a Malignancy]} urw:hasUncertainty  highProbability.
#  
#  # The findings are suspicious for malignancy.
#  theLesion hasFeature X, Y.
{theLesion hasFeature X, Y} suggests {thePatient :has [a Malignancy]}. 
#  
#  # The mass is suspicious for malignancy.
#  theMass hasAppearance malignantAppearance.
#  
#  # The patient's category is Suspicious for Malignancy.
#  thePatient diagnosticCategory SuspiciousForMalignancy.
#  
#  # The diagnosis is: "Suspicious for Malignancy".
#  theDiagnosis = "Suspicious for Malignancy".
#  
#  # The diagnosis category is Suspicious for Malignancy.
#  theDiagnosis :diagnosticCategory SuspiciousForMalignancy.
#  
#  # The report category is Suspicious for Malignancy.
#  <http://theHospital.example/2009/01/01/12345678>
#  
#  # This patient should be managed according to the
#  
# applicable Suspicious for Malignancy protocol.
#  # ???????
#  
#  
#  # end more from the CSHALS
#  	
#  
#  # =====================================================================
#  # INTERNAL AXIOMS: Some assertions regarding the document-only resources in
#  # this interpretation
#  Patient rdf:subClassOf foaf:Person.
#  Patient a skos:Concept;
#   skos:label "patient".
#  MammogramReport a foaf:Document.
#  
#  
#  # =====================================================================
#  # BACKGROUND AXIOMS: Some assertions regarding the background knowledge
#  # assumed by the interpreter (i.e. me, not the author)