--- a/syntheticPatients/AD_PCHR_1-indivo.xml Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/AD_PCHR_1-indivo.xml Mon Oct 04 11:47:45 2010 -0400
@@ -544,19 +544,12 @@
</Encounter>
<Encounter>
<Date>2009-07-15</Date>
- <Date>2009-07-16</Date>
<Contact>
<fullName>Henry No</fullName>
</Contact>
- <Contact>
- <fullName>Mark Tourney</fullName>
- </Contact>
- <MedicalBaseline>false</MedicalBaseline>
<MedicalBaseline>false</MedicalBaseline>
<MedicalTest>false</MedicalTest>
- <MedicalTest>true</MedicalTest>
<ReportedSymptoms>Confusion, Declining memory</ReportedSymptoms>
- <ReportedSymptoms> Confusion, Declining memory </ReportedSymptoms>
<WorkingDiagnosis>
<PreliminaryDiagnosis>
<DiagnosisDescription>Dementia</DiagnosisDescription>
@@ -566,6 +559,16 @@
<DifferentialDiagnosis>
</DifferentialDiagnosis>
</WorkingDiagnosis>
+ <LabTests/>
+ </Encounter>
+ <Encounter>
+ <Date>2009-07-16</Date>
+ <Contact>
+ <fullName>Mark Tourney</fullName>
+ </Contact>
+ <MedicalBaseline>false</MedicalBaseline>
+ <MedicalTest>true</MedicalTest>
+ <ReportedSymptoms> Confusion, Declining memory </ReportedSymptoms>
<WorkingDiagnosis>
<PreliminaryDiagnosis>
<DiagnosisDescription>Dementia</DiagnosisDescription>
@@ -579,7 +582,7 @@
</WorkingDiagnosis>
<LabTests>
<Test>
- <dateMeasured>2009-07-15</dateMeasured>
+ <dateMeasured>2009-07-16</dateMeasured>
<name>Other psychologic evaluation and testing</name>
<HCLSresult>
<LabTest>
@@ -589,7 +592,7 @@
<status>@@@</status>
</Test>
<Test>
- <dateMeasured>2009-07-15</dateMeasured>
+ <dateMeasured>2009-07-16</dateMeasured>
<name>Magnetic resonance imaging of brain and brain</name>
<HCLSresult>
<LabTest>
@@ -599,12 +602,12 @@
<status>@@@</status>
</Test>
<Test>
- <dateMeasured>2009-07-15</dateMeasured>
+ <dateMeasured>2009-07-16</dateMeasured>
<name>Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count</name>
<status>@@@</status>
</Test>
<Test>
- <dateMeasured>2009-07-15</dateMeasured>
+ <dateMeasured>2009-07-16</dateMeasured>
<name>ADmark Alzheimer's Evaluation</name>
<SNPresult>
<LabTest>
--- a/syntheticPatients/AD_PCHR_1-tmo.trig Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/AD_PCHR_1-tmo.trig Mon Oct 04 11:47:45 2010 -0400
@@ -42,41 +42,43 @@
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "2009-05-15"^^xsd:dateTime ;
+ trans:prescribedOn "2009-05-15" ;
trans:genericName "COREG TABLETS" ;
] .
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "2009-05-20"^^xsd:dateTime ;
+ trans:prescribedOn "2009-05-20" ;
trans:genericName "LIPITOR TABLETS" ;
] .
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "2009-05-20"^^xsd:dateTime ;
+ trans:prescribedOn "2009-05-20" ;
trans:genericName "COUMADIN TABLETS" ;
] .
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "2009-08-10"^^xsd:dateTime ;
+ trans:prescribedOn "2009-08-10" ;
+
+ trans:datePrescriptionEnded "2009-08-15" ;
trans:genericName "DONEPEZIL HYDROCHLORIDE TABLETS" ;
] .
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "2009-08-15"^^xsd:dateTime ;
+ trans:prescribedOn "2009-08-15" ;
trans:genericName "ARICEPT TABLETS ORALLY DISINTEGRATING" ;
] .
_:patient trans:hasCondition [
- trans:onset "2009-05-15T12:00:00"^^xsd:dateTime ;
+ trans:onset "2009-05-15T12:00:00" ;
trans:diagnosedWith "hypertension" ;
@@ -85,7 +87,7 @@
] .
_:patient trans:hasCondition [
- trans:onset "2009-05-20T12:00:00"^^xsd:dateTime ;
+ trans:onset "2009-05-20T12:00:00" ;
trans:diagnosedWith "hypercholesterolaemia" ;
@@ -94,7 +96,7 @@
] .
_:patient trans:hasCondition [
- trans:onset "2009-05-20T12:00:00"^^xsd:dateTime ;
+ trans:onset "2009-05-20T12:00:00" ;
trans:diagnosedWith "atrial fibrillation" ;
@@ -103,7 +105,7 @@
] .
_:patient trans:hasCondition [
- trans:onset "2009-08-10T12:00:00"^^xsd:dateTime ;
+ trans:onset "2009-08-10T12:00:00" ;
trans:diagnosedWith "alzheimer’s disease" ;
@@ -113,7 +115,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-05-15"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-05-15" ;
trans:workingDiagnosis "false" ;
@@ -123,7 +125,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-05-17"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-05-17" ;
trans:workingDiagnosis "atrial fibrillation" ;
@@ -133,7 +135,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-05-18"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-05-18" ;
trans:workingDiagnosis "atrial fibrillation" ;
@@ -143,17 +145,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-05-20"^^xsd:dateTime ;
-
- trans:workingDiagnosis "none" ;
-
- trans:reportedSymptoms "none"
-
- ] .
-
- [ a trans:Encounter ;
- trans:patient _:patient ;
- trans:dateOfEncounter "2009-06-03"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-05-20" ;
trans:workingDiagnosis "none" ;
@@ -163,7 +155,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-07-03"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-06-03" ;
trans:workingDiagnosis "none" ;
@@ -173,9 +165,17 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-07-15"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-07-03" ;
- trans:workingDiagnosis "Dementia" ;
+ trans:workingDiagnosis "none" ;
+
+ trans:reportedSymptoms "none"
+
+ ] .
+
+ [ a trans:Encounter ;
+ trans:patient _:patient ;
+ trans:dateOfEncounter "2009-07-15" ;
trans:workingDiagnosis "Dementia" ;
@@ -185,7 +185,17 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-08-03"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-07-16" ;
+
+ trans:workingDiagnosis "Dementia" ;
+
+ trans:reportedSymptoms " Confusion, Declining memory "
+
+ ] .
+
+ [ a trans:Encounter ;
+ trans:patient _:patient ;
+ trans:dateOfEncounter "2009-08-03" ;
trans:workingDiagnosis "false" ;
@@ -195,7 +205,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-08-15"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-08-15" ;
trans:workingDiagnosis "adverse event to Donepezil" ;
@@ -205,7 +215,7 @@
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "2009-11-03"^^xsd:dateTime ;
+ trans:dateOfEncounter "2009-11-03" ;
trans:workingDiagnosis "false" ;
--- a/syntheticPatients/AD_PCHR_1.xml Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/AD_PCHR_1.xml Mon Oct 04 11:47:45 2010 -0400
@@ -860,6 +860,9 @@
</differentialDiagnosis>
</workingDiagnosis>
+<!-- I *think* this was supposed to be two encounters. -->
+</Encounter>
+<Encounter>
<dateOfEncounter>2009-07-16</dateOfEncounter>
<physician>Mark Tourney</physician>
--- a/syntheticPatients/Indivo2Trig.xsl Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/Indivo2Trig.xsl Mon Oct 04 11:47:45 2010 -0400
@@ -86,9 +86,9 @@
<xsl:template match="in:Prescription">
[ a trans:Prescription ;
trans:prescribedTo _:patient ;
- trans:prescribedOn "<xsl:value-of select="in:medication/in:dateStarted"/>"^^xsd:dateTime ; <!-- trans:dateStarted -->
-<xsl:if test="in:medication/dateStopped">
- trans:datePrescriptionEnded "<xsl:value-of select="in:medication/in:dateStopped"/>"^^xsd:dateTime ;
+ trans:prescribedOn <xsl:apply-templates mode="date" select="in:medication/in:dateStarted"/> ; <!-- trans:dateStarted -->
+<xsl:if test="in:medication/in:dateStopped">
+ trans:datePrescriptionEnded <xsl:apply-templates mode="date" select="in:medication/in:dateStopped"/> ;
</xsl:if>
trans:genericName "<xsl:value-of select="in:medication/in:genericName"/>" ;
] .
@@ -104,7 +104,7 @@
</xsl:template>
<xsl:template mode="problem" match="in:dateOnset">
- trans:onset "<xsl:value-of select="text()"/>"^^xsd:dateTime ;
+ trans:onset <xsl:apply-templates mode="date" select="."/> ;
</xsl:template>
<xsl:template mode="problem" match="in:name">
@@ -118,7 +118,7 @@
<xsl:template match="in:Encounter">
[ a trans:Encounter ;
trans:patient _:patient ;
- trans:dateOfEncounter "<xsl:value-of select="in:Date/text()"/>"^^xsd:dateTime ;
+ trans:dateOfEncounter <xsl:apply-templates mode="date" select="in:Date"/> ;
<xsl:apply-templates select="in:WorkingDiagnosis/in:PreliminaryDiagnosis"/>
trans:reportedSymptoms "<xsl:value-of select="in:ReportedSymptoms/text()"/>"
@@ -129,4 +129,9 @@
trans:workingDiagnosis "<xsl:value-of select="in:DiagnosisDescription/text()"/>" ;
</xsl:template>
+<!-- Utility templates
+-->
+
+<xsl:template mode="date" match="*">"<xsl:value-of select="text()"/>"<!-- ^^xsd:dateTime --></xsl:template>
+
</xsl:stylesheet>
\ No newline at end of file
--- a/syntheticPatients/Makefile Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/Makefile Mon Oct 04 11:47:45 2010 -0400
@@ -51,7 +51,7 @@
$(SPARQL) -qd $(word 1, $^) -e 'PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?mbox { ?s foaf:mbox ?mbox }' --compare $(word 2, $^) || echo $<\(0\): error !mbox
q1_%: AD_PCHR_%-tmo.trig tests/q1.rq tests/q1_%.srt
- $(SPARQL) -g pchr $(word 1, $^) $(word 2, $^) --compare $(word 3, $^) || echo $<\(0\): error !q1
+ $(SPARQL) -qg pchr $(word 1, $^) $(word 2, $^) --compare $(word 3, $^) || echo $<\(0\): error !q1
test: all $(MBOXES) $(Q1S)
--- a/syntheticPatients/tests/q1.rq Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/tests/q1.rq Mon Oct 04 11:47:45 2010 -0400
@@ -12,9 +12,9 @@
trans:dateOfEncounter ?encounter_date .
?drug trans:prescribedTo ?patient ; # dateStarted
trans:prescribedOn ?prescription_start;
-# trans:datePrescriptionEnded ?prescription_end;
-# trans:genericName ?drug_name
-# FILTER regex(?drug_name,"DONEPEZIL","i").
-# FILTER (?prescription_start <= ?encounter_date && ?prescription_end >= ?encounter_date)
+ trans:datePrescriptionEnded ?prescription_end;
+ trans:genericName ?drug_name
+ FILTER regex(?drug_name,"DONEPEZIL","i").
+ FILTER (?prescription_start <= ?encounter_date && ?prescription_end >= ?encounter_date)
}
}
--- a/syntheticPatients/tests/q1_1.srt Sun Oct 03 23:05:34 2010 -0400
+++ b/syntheticPatients/tests/q1_1.srt Mon Oct 04 11:47:45 2010 -0400
@@ -1,4 +1,4 @@
-+--------------------+----------------------+-----------------+-----------+------------------------------+-----------------------------------+---------------------+
-| ?patient | ?patient_name | ?encounter_date | ?symptoms | ?diagnosis | ?drug_name | ?prescription_start |
-| <AD_PCHR_1.rdf#me> | "George Andrew Tour" | "2009-08-15" | "nausea" | "adverse event to Donepezil" | "DONEPEZIL HYDROCHLORIDE TABLETS" | "2009-08-10" |
-+--------------------+----------------------+-----------------+-----------+------------------------------+-----------------------------------+---------------------+
++----------+----------------------+-----------------+-----------+------------------------------+-----------------------------------+---------------------+
+| ?patient | ?patient_name | ?encounter_date | ?symptoms | ?diagnosis | ?drug_name | ?prescription_start |
+| _:x | "George Andrew Tour" | "2009-08-15" | "nausea" | "adverse event to Donepezil" | "DONEPEZIL HYDROCHLORIDE TABLETS" | "2009-08-10" |
++----------+----------------------+-----------------+-----------+------------------------------+-----------------------------------+---------------------+