changed :variant to :feature in Indivo2Trig.xsl and q6.rq; including patient trig files
authorTim L <lebot@rpi.edu>
Mon, 07 Feb 2011 07:23:06 -0500
changeset 38 c903152963c8
parent 37 1f34c9bd8fdf
child 39 9c504d3bdf5e
changed :variant to :feature in Indivo2Trig.xsl and q6.rq; including patient trig files
syntheticPatients/AD_PCHR_1-tmo.trig
syntheticPatients/AD_PCHR_2-tmo.trig
syntheticPatients/AD_PCHR_3-tmo.trig
syntheticPatients/AD_PCHR_4-tmo.trig
syntheticPatients/AD_PCHR_5-tmo.trig
syntheticPatients/AD_PCHR_6-tmo.trig
syntheticPatients/AD_PCHR_7-tmo.trig
syntheticPatients/Indivo2Trig.xsl
syntheticPatients/tests/q6.rq
--- a/syntheticPatients/AD_PCHR_1-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_1-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -115,53 +117,63 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-05-15T12:00:00" ;
 
-  trans:diagnosedWith "hypertension" ;
+  trans:diagnosedWith :hypertension ;
   trans:ICD9 "410" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypertension dct:identifier "hypertension" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-05-20T12:00:00" ;
 
-  trans:diagnosedWith "hypercholesterolaemia" ;
+  trans:diagnosedWith :hypercholesterolaemia ;
   trans:ICD9 "272" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypercholesterolaemia dct:identifier "hypercholesterolaemia" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-05-17T12:00:00" ;
 
-  trans:diagnosedWith "atrial fibrillation" ;
+  trans:diagnosedWith :atrial_fibrillation ;
   trans:ICD9 "427" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:atrial_fibrillation dct:identifier "atrial fibrillation" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-07-15T12:00:00" ;
 
-  trans:diagnosedWith "dementia" ;
+  trans:diagnosedWith :dementia ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:dementia dct:identifier "dementia" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-07-16T12:00:00" ;
 
-  trans:diagnosedWith "alzheimer’s disease" ;
+  trans:diagnosedWith :alzheimers_disease ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_disease dct:identifier "alzheimer’s disease" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2009-05-15" ;
@@ -228,25 +240,55 @@
 
     trans:test [
         # indivo:dateMeasured "2009-05-18" ;
-        trans:testName "Warfarin Sensitivity" ;
+        a :Warfarin_Sensitivity ;
         
-    trans:result [
-        trans:variant_Synonyms "VKOR; MST134; MST576; VKCFD2; EDTP308; MGC2694; FLJ00289; IMAGE345520" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_VKOR ;
+           trans:present true ;
+       ] ;
 
     ] ;
 
     trans:test [
         # indivo:dateMeasured "2009-05-18" ;
-        trans:testName "Warfarin Sensitivity" ;
+        a :Warfarin_Sensitivity ;
         
-    trans:result [
-        trans:variant_Synonyms " CPC9; CYP2C; CYP2C10; MGC88320; P450IIC9; MGC149605; CYP2C9 " ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_CPC9 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_VKOR skos:relatedMatch :variant_MST134 .
+:variant_MST134 dct:identifier "MST134" .
+:variant_VKOR skos:relatedMatch :variant_MST576 .
+:variant_MST576 dct:identifier "MST576" .
+:variant_VKOR skos:relatedMatch :variant_VKCFD2 .
+:variant_VKCFD2 dct:identifier "VKCFD2" .
+:variant_VKOR skos:relatedMatch :variant_EDTP308 .
+:variant_EDTP308 dct:identifier "EDTP308" .
+:variant_VKOR skos:relatedMatch :variant_MGC2694 .
+:variant_MGC2694 dct:identifier "MGC2694" .
+:variant_VKOR skos:relatedMatch :variant_FLJ00289 .
+:variant_FLJ00289 dct:identifier "FLJ00289" .
+:variant_VKOR skos:relatedMatch :variant_IMAGE345520 .
+:variant_IMAGE345520 dct:identifier "IMAGE345520" .
+:variant_CPC9 skos:relatedMatch :variant_CYP2C .
+:variant_CYP2C dct:identifier "CYP2C" .
+:variant_CPC9 skos:relatedMatch :variant_CYP2C10 .
+:variant_CYP2C10 dct:identifier "CYP2C10" .
+:variant_CPC9 skos:relatedMatch :variant_MGC88320 .
+:variant_MGC88320 dct:identifier "MGC88320" .
+:variant_CPC9 skos:relatedMatch :variant_P450IIC9 .
+:variant_P450IIC9 dct:identifier "P450IIC9" .
+:variant_CPC9 skos:relatedMatch :variant_MGC149605 .
+:variant_MGC149605 dct:identifier "MGC149605" .
+:variant_CPC9 skos:relatedMatch :variant_CYP2C9 .
+:variant_CYP2C9 dct:identifier "CYP2C9" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
@@ -328,15 +370,19 @@
 
     trans:test [
         # indivo:dateMeasured "2009-07-16" ;
-        trans:testName "ADmark Alzheimer's Evaluation" ;
+        a :ADmark_Alzheimers_Evaluation ;
         
-    trans:result [
-        trans:variant_Synonyms "APOE4, NG_007084.2:g.7903T>C" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_APOE4 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_APOE4 skos:relatedMatch :variant_NG_007084_2_g_7903T_C .
+:variant_NG_007084_2_g_7903T_C dct:identifier "NG_007084.2:g.7903T>C" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
--- a/syntheticPatients/AD_PCHR_2-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_2-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -138,53 +140,63 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2004-07-10T12:00:00" ;
 
-  trans:diagnosedWith "mild cognitive impairment" ;
+  trans:diagnosedWith :mild_cognitive_impairment ;
   trans:ICD9 "290.0" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:mild_cognitive_impairment dct:identifier "mild cognitive impairment" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2007-07-20T12:00:00" ;
 
-  trans:diagnosedWith "hypercholesterolaemia" ;
+  trans:diagnosedWith :hypercholesterolaemia ;
   trans:ICD9 "272" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypercholesterolaemia dct:identifier "hypercholesterolaemia" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2008-03-18T12:00:00" ;
 
-  trans:diagnosedWith "myocardial infarction" ;
+  trans:diagnosedWith :myocardial_infarction ;
   trans:ICD9 "410.3" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:myocardial_infarction dct:identifier "myocardial infarction" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2008-05-16T12:00:00" ;
 
-  trans:diagnosedWith "anxiety depression" ;
+  trans:diagnosedWith :anxiety_depression ;
   trans:ICD9 "300.4" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:anxiety_depression dct:identifier "anxiety depression" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-10-15T12:00:00" ;
 
-  trans:diagnosedWith "alzheimer’s disease" ;
+  trans:diagnosedWith :alzheimers_disease ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_disease dct:identifier "alzheimer’s disease" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2004-07-10" ;
@@ -267,11 +279,13 @@
 
     trans:test [
         # indivo:dateMeasured "2004-10-01" ;
-        trans:testName "ADmark Alzheimer's Evaluation" ;
+        a :ADmark_Alzheimers_Evaluation ;
         
-    trans:result [
-        trans:variant_Synonyms "APOE4, NG_007084.2:g.7903T>C" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_APOE4 ;
+           trans:present true ;
+       ] ;
 
     ] ;
 
@@ -306,6 +320,8 @@
     ] ;
     
   ] .
+:variant_APOE4 skos:relatedMatch :variant_NG_007084_2_g_7903T_C .
+:variant_NG_007084_2_g_7903T_C dct:identifier "NG_007084.2:g.7903T>C" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
@@ -739,15 +755,27 @@
 
     trans:test [
         # indivo:dateMeasured "2008-03-19" ;
-        trans:testName "" ;
+        a : ;
         
-    trans:result [
-        trans:variant_Synonyms "CYP2C19; RP11-400G3.4, CPCJ, CYP2C, P450C2C, P450IIC19" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_CYP2C19 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_CYP2C19 skos:relatedMatch :variant_RP11-400G3_4 .
+:variant_RP11-400G3_4 dct:identifier "RP11-400G3.4" .
+:variant_CYP2C19 skos:relatedMatch :variant_CPCJ .
+:variant_CPCJ dct:identifier "CPCJ" .
+:variant_CYP2C19 skos:relatedMatch :variant_CYP2C .
+:variant_CYP2C dct:identifier "CYP2C" .
+:variant_CYP2C19 skos:relatedMatch :variant_P450C2C .
+:variant_P450C2C dct:identifier "P450C2C" .
+:variant_CYP2C19 skos:relatedMatch :variant_P450IIC19 .
+:variant_P450IIC19 dct:identifier "P450IIC19" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
@@ -775,15 +803,35 @@
 
     trans:test [
         # indivo:dateMeasured "2008-05-17" ;
-        trans:testName "" ;
+        a : ;
         
-    trans:result [
-        trans:variant_Synonyms " RP4-669P10.2, CPD6, CYP2D, [email protected], CYP2DL1, MGC120389, MGC120390, P450-DB1, P450C2D, P450DB1" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_RP4-669P10_2 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_CPD6 .
+:variant_CPD6 dct:identifier "CPD6" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_CYP2D .
+:variant_CYP2D dct:identifier "CYP2D" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_CYP2D_ .
+:variant_CYP2D_ dct:identifier "[email protected]" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_CYP2DL1 .
+:variant_CYP2DL1 dct:identifier "CYP2DL1" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_MGC120389 .
+:variant_MGC120389 dct:identifier "MGC120389" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_MGC120390 .
+:variant_MGC120390 dct:identifier "MGC120390" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_P450-DB1 .
+:variant_P450-DB1 dct:identifier "P450-DB1" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_P450C2D .
+:variant_P450C2D dct:identifier "P450C2D" .
+:variant_RP4-669P10_2 skos:relatedMatch :variant_P450DB1 .
+:variant_P450DB1 dct:identifier "P450DB1" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
--- a/syntheticPatients/AD_PCHR_3-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_3-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -121,33 +123,39 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2001-01-03T12:00:00" ;
 
-  trans:diagnosedWith "Osteoarthrosis generalized involving hand" ;
+  trans:diagnosedWith :osteoarthrosis_generalized_involving_hand ;
   trans:ICD9 "715.04" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:osteoarthrosis_generalized_involving_hand dct:identifier "Osteoarthrosis generalized involving hand" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2005-11-03T12:00:00" ;
 
-  trans:diagnosedWith "Alzheimer's Disease" ;
+  trans:diagnosedWith :alzheimers_disease ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_disease dct:identifier "Alzheimer's Disease" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2007-09-23T12:00:00" ;
 
-  trans:diagnosedWith "Dyspepsia and other specified disorders of stomach" ;
+  trans:diagnosedWith :dyspepsia_and_other_specified_disorders_of_stomach ;
   trans:ICD9 "536.8" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:dyspepsia_and_other_specified_disorders_of_stomach dct:identifier "Dyspepsia and other specified disorders of stomach" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "1996-09-12" ;
--- a/syntheticPatients/AD_PCHR_4-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_4-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -91,33 +93,39 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "1950-05-15T12:00:00" ;
 
-  trans:diagnosedWith "Epilepsy and recurrent seizures" ;
+  trans:diagnosedWith :epilepsy_and_recurrent_seizures ;
   trans:ICD9 "345" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:epilepsy_and_recurrent_seizures dct:identifier "Epilepsy and recurrent seizures" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "1995-05-20T12:00:00" ;
 
-  trans:diagnosedWith "Hypertension" ;
+  trans:diagnosedWith :hypertension ;
   trans:ICD9 "402.1" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypertension dct:identifier "Hypertension" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-05-20T12:00:00" ;
 
-  trans:diagnosedWith "Alzheimer’s Dementia" ;
+  trans:diagnosedWith :alzheimers_dementia ;
   trans:ICD9 "331.0" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_dementia dct:identifier "Alzheimer’s Dementia" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2001-06-15" ;
@@ -258,14 +266,18 @@
 
     trans:test [
         # indivo:dateMeasured "2009-07-16" ;
-        trans:testName "ADmark Alzheimer's Evaluation" ;
+        a :ADmark_Alzheimers_Evaluation ;
         
-    trans:result [
-        trans:variant_Synonyms "APOE4, NG_007084.2:g.7903T>C" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_APOE4 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_APOE4 skos:relatedMatch :variant_NG_007084_2_g_7903T_C .
+:variant_NG_007084_2_g_7903T_C dct:identifier "NG_007084.2:g.7903T>C" .
 
 }
--- a/syntheticPatients/AD_PCHR_5-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_5-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -115,63 +117,75 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2008-02-03T12:00:00" ;
 
-  trans:diagnosedWith "hypertension" ;
+  trans:diagnosedWith :hypertension ;
   trans:ICD9 "410" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypertension dct:identifier "hypertension" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-07-21T12:00:00" ;
 
-  trans:diagnosedWith "alzheimer’s disease" ;
+  trans:diagnosedWith :alzheimers_disease ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_disease dct:identifier "alzheimer’s disease" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2008-05-06T12:00:00" ;
 
-  trans:diagnosedWith "acute coronary occlusion without myocardial infarction" ;
+  trans:diagnosedWith :acute_coronary_occlusion_without_myocardial_infarction ;
   trans:ICD9 "414" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:acute_coronary_occlusion_without_myocardial_infarction dct:identifier "acute coronary occlusion without myocardial infarction" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-06-18T12:00:00" ;
 
-  trans:diagnosedWith "gastroesophageal reflux disease" ;
+  trans:diagnosedWith :gastroesophageal_reflux_disease ;
   trans:ICD9 "530.81" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:gastroesophageal_reflux_disease dct:identifier "gastroesophageal reflux disease" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-07-23T12:00:00" ;
 
-  trans:diagnosedWith "nausea and vomiting" ;
+  trans:diagnosedWith :nausea_and_vomiting ;
   trans:ICD9 "787.0" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:nausea_and_vomiting dct:identifier "nausea and vomiting" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-07-23T12:00:00" ;
 
-  trans:diagnosedWith "adverse drug effect" ;
+  trans:diagnosedWith :adverse_drug_effect ;
   trans:ICD9 "9995.2" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:adverse_drug_effect dct:identifier "adverse drug effect" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2002-02-02" ;
--- a/syntheticPatients/AD_PCHR_6-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_6-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -82,23 +84,27 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2008-11-09T12:00:00" ;
 
-  trans:diagnosedWith "Hypertension" ;
+  trans:diagnosedWith :hypertension ;
   trans:ICD9 "401.9" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypertension dct:identifier "Hypertension" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-11-09T12:00:00" ;
 
-  trans:diagnosedWith "Hypocalcemia" ;
+  trans:diagnosedWith :hypocalcemia ;
   trans:ICD9 "275.41" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:hypocalcemia dct:identifier "Hypocalcemia" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2009-05-10" ;
@@ -183,15 +189,19 @@
 
     trans:test [
         # indivo:dateMeasured "2009-07-20" ;
-        trans:testName "ADmark Alzheimer's Evaluation" ;
+        a :ADmark_Alzheimers_Evaluation ;
         
-    trans:result [
-        trans:variant_Synonyms "APOE4, NG_007084.2:g.7903T>C" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_APOE4 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_APOE4 skos:relatedMatch :variant_NG_007084_2_g_7903T_C .
+:variant_NG_007084_2_g_7903T_C dct:identifier "NG_007084.2:g.7903T>C" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
--- a/syntheticPatients/AD_PCHR_7-tmo.trig	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/AD_PCHR_7-tmo.trig	Mon Feb 07 07:23:06 2011 -0500
@@ -7,6 +7,8 @@
   @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/> .
 {
   <> a cpr:patient-record .
   _:patient cpr:subjectOfDescription <> .
@@ -58,23 +60,27 @@
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "1978-01-31T12:00:00" ;
 
-  trans:diagnosedWith "Down Syndrome" ;
+  trans:diagnosedWith :down_syndrome ;
   trans:ICD9 "758" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:down_syndrome dct:identifier "Down Syndrome" .
+
   _:patient trans:hasCondition [
   cpr:startsNoLaterThan "2009-02-01T12:00:00" ;
 
-  trans:diagnosedWith "Alzheimer’s Disease" ;
+  trans:diagnosedWith :alzheimers_disease ;
   trans:ICD9 "331" ;
 
   # unmatched comments
   # unmatched diagnosedBy
   ] .
 
+:alzheimers_disease dct:identifier "Alzheimer’s Disease" .
+
   [ a trans:Encounter ;
     trans:patient _:patient ;
     trans:dateOfEncounter "2008-11-15" ;
@@ -171,15 +177,19 @@
 
     trans:test [
         # indivo:dateMeasured "2009-01-20" ;
-        trans:testName "ADmark Alzheimer's Evaluation" ;
+        a :ADmark_Alzheimers_Evaluation ;
         
-    trans:result [
-        trans:variant_Synonyms "APOE4, NG_007084.2:g.7903T>C" ;
-    ] ;
+       trans:result [
+           a :SNPResult ;
+           trans:feature :variant_APOE4 ;
+           trans:present true ;
+       ] ;
 
     ] ;
     
   ] .
+:variant_APOE4 skos:relatedMatch :variant_NG_007084_2_g_7903T_C .
+:variant_NG_007084_2_g_7903T_C dct:identifier "NG_007084.2:g.7903T>C" .
 
   [ a trans:Encounter ;
     trans:patient _:patient ;
--- a/syntheticPatients/Indivo2Trig.xsl	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/Indivo2Trig.xsl	Mon Feb 07 07:23:06 2011 -0500
@@ -211,7 +211,7 @@
    <xsl:variable name="primary-synonym"   select="concat('variant_',translate($primary-synonymL,'>.:@','____'))"/>
        trans:result [
            a :SNPResult ;
-           trans:variant :<xsl:value-of select="$primary-synonym"/> ;
+           trans:feature :<xsl:value-of select="$primary-synonym"/> ;
            trans:present true ;
        ] ;
 </xsl:template>
--- a/syntheticPatients/tests/q6.rq	Sun Feb 06 23:29:15 2011 -0500
+++ b/syntheticPatients/tests/q6.rq	Mon Feb 07 07:23:06 2011 -0500
@@ -1,7 +1,3 @@
-PREFIX trans: <tag:[email protected]:2009/tmo/translator#>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-
-
 # Before Tim started doing stuff:
 #WHERE {
 # ?encounter trans:patient ?patient .
@@ -18,6 +14,9 @@
 # FILTER (regex (?apoe4, "APOE4"))
 #}
 
+PREFIX trans: <tag:[email protected]:2009/tmo/translator#>
+PREFIX foaf:  <http://xmlns.com/foaf/0.1/>
+
 SELECT distinct ?patient ?name
 WHERE {
 
@@ -34,7 +33,7 @@
          trans:result ?result
       ] . 
       ?result
-            trans:variant trans:variant_APOE4;
+            trans:feature trans:variant_APOE4;
             trans:present true
    }
    FILTER(!bound(?result))