| [1571] | 1 | C0SLAB ; GPL - Smart Lab Processing ;4/15/12 17:05
|
|---|
| [1591] | 2 | ;;1.0;VISTA SMART CONTAINER;;Sep 26, 2012;Build 5
|
|---|
| 3 | ;Copyright 2012 George Lilly.
|
|---|
| [1571] | 4 | ;
|
|---|
| [1591] | 5 | ; This program is free software: you can redistribute it and/or modify
|
|---|
| 6 | ; it under the terms of the GNU Affero General Public License as
|
|---|
| 7 | ; published by the Free Software Foundation, either version 3 of the
|
|---|
| 8 | ; License, or (at your option) any later version.
|
|---|
| [1571] | 9 | ;
|
|---|
| [1591] | 10 | ; This program is distributed in the hope that it will be useful,
|
|---|
| 11 | ; but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|---|
| 12 | ; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|---|
| 13 | ; GNU Affero General Public License for more details.
|
|---|
| [1571] | 14 | ;
|
|---|
| [1591] | 15 | ; You should have received a copy of the GNU Affero General Public License
|
|---|
| 16 | ; along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|---|
| [1571] | 17 | ;
|
|---|
| 18 | Q
|
|---|
| 19 | ;
|
|---|
| 20 | ; sample VistA NHIN lab result
|
|---|
| 21 | ;
|
|---|
| 22 | ;^TMP("C0STBL",32,"lab",8,"collected@value")=3110626.16
|
|---|
| 23 | ;^TMP("C0STBL",32,"lab",8,"comment")="Report Released Date/Time: Jun 26, 2011@19:00"
|
|---|
| 24 | ;^TMP("C0STBL",32,"lab",8,"comment@xml:space")="preserve"
|
|---|
| 25 | ;^TMP("C0STBL",32,"lab",8,"facility@code")=100
|
|---|
| 26 | ;^TMP("C0STBL",32,"lab",8,"facility@name")="VOE OFFICE INSTITUTION"
|
|---|
| 27 | ;^TMP("C0STBL",32,"lab",8,"groupName@value")="CH 0626 47"
|
|---|
| 28 | ;^TMP("C0STBL",32,"lab",8,"high@value")=" 101"
|
|---|
| 29 | ;^TMP("C0STBL",32,"lab",8,"id@value")="CH;6889372.84;67003"
|
|---|
| 30 | ;^TMP("C0STBL",32,"lab",8,"interpretation@value")="H"
|
|---|
| 31 | ;^TMP("C0STBL",32,"lab",8,"labOrderID@value")=336
|
|---|
| 32 | ;^TMP("C0STBL",32,"lab",8,"localName@value")="FBLDGLU"
|
|---|
| 33 | ;^TMP("C0STBL",32,"lab",8,"loinc@value")="14771-0"
|
|---|
| 34 | ;^TMP("C0STBL",32,"lab",8,"low@value")="69 "
|
|---|
| 35 | ;^TMP("C0STBL",32,"lab",8,"orderID@value")=807
|
|---|
| 36 | ;^TMP("C0STBL",32,"lab",8,"result@value")=178
|
|---|
| 37 | ;^TMP("C0STBL",32,"lab",8,"resulted@value")=3110626.190006
|
|---|
| 38 | ;^TMP("C0STBL",32,"lab",8,"sample@value")="SERUM"
|
|---|
| 39 | ;^TMP("C0STBL",32,"lab",8,"specimen@code")="0X500"
|
|---|
| 40 | ;^TMP("C0STBL",32,"lab",8,"specimen@name")="SERUM"
|
|---|
| 41 | ;^TMP("C0STBL",32,"lab",8,"status@value")="completed"
|
|---|
| 42 | ;^TMP("C0STBL",32,"lab",8,"test@value")="FASTING BLOOD GLUCOSE"
|
|---|
| 43 | ;^TMP("C0STBL",32,"lab",8,"type@value")="CH"
|
|---|
| 44 | ;^TMP("C0STBL",32,"lab",8,"units@value")="MG/DL"
|
|---|
| 45 | ;^TMP("C0STBL",32,"lab",8,"vuid@value")=4656342
|
|---|
| 46 | ;
|
|---|
| 47 | ; sample Smart lab result triples
|
|---|
| 48 | ;
|
|---|
| 49 | ;G("loinc:29571-7","dcterms:identifier")="29571-7"
|
|---|
| 50 | ;G("loinc:29571-7","dcterms:title")="Phe DBS Ql"
|
|---|
| 51 | ;G("loinc:29571-7","rdf:type")="sp:Code"
|
|---|
| 52 | ;G("loinc:29571-7","sp:system")="http://loinc.org/codes/"
|
|---|
| 53 | ;G("loinc:38478-4","dcterms:identifier")="38478-4"
|
|---|
| 54 | ;G("loinc:38478-4","dcterms:title")="Biotinidase DBS Ql"
|
|---|
| 55 | ;G("loinc:38478-4","rdf:type")="sp:Code"
|
|---|
| 56 | ;G("loinc:38478-4","sp:system")="http://loinc.org/codes/"
|
|---|
| 57 | ;G("qqWZZIew993","rdf:type")="sp:Attribution"
|
|---|
| 58 | ;G("qqWZZIew993","sp:startDate")="2007-04-21"
|
|---|
| 59 | ;G("qqWZZIew994","rdf:type")="sp:NarrativeResult"
|
|---|
| 60 | ;G("qqWZZIew994","sp:value")="Normal"
|
|---|
| 61 | ;G("qqWZZIew995","dcterms:title")="Biotinidase DBS Ql"
|
|---|
| 62 | ;G("qqWZZIew995","rdf:type")="sp:CodedValue"
|
|---|
| 63 | ;G("qqWZZIew995","sp:code")="loinc:38478-4"
|
|---|
| 64 | ;G("qqWZZIew997","rdf:type")="sp:Attribution"
|
|---|
| 65 | ;G("qqWZZIew997","sp:startDate")="2007-09-08"
|
|---|
| 66 | ;G("qqWZZIew998","rdf:type")="sp:NarrativeResult"
|
|---|
| 67 | ;G("qqWZZIew998","sp:value")="Normal"
|
|---|
| 68 | ;G("qqWZZIew999","dcterms:title")="Phe DBS Ql"
|
|---|
| 69 | ;G("qqWZZIew999","rdf:type")="sp:CodedValue"
|
|---|
| 70 | ;G("qqWZZIew999","sp:code")="loinc:29571-7"
|
|---|
| 71 | ;G("smart:99912345/lab_results/3d9b39249193","rdf:type")="sp:LabResult"
|
|---|
| 72 | ;G("smart:99912345/lab_results/3d9b39249193","sp:belongsTo")="smart:99912345"
|
|---|
| 73 | ;G("smart:99912345/lab_results/3d9b39249193","sp:labName")="qqWZZIew995"
|
|---|
| 74 | ;G("smart:99912345/lab_results/3d9b39249193","sp:narrativeResult")="qqWZZIew994"
|
|---|
| 75 | ;G("smart:99912345/lab_results/3d9b39249193","sp:specimenCollected")="qqWZZIew993"
|
|---|
| 76 | ;G("smart:99912345/lab_results/426c7adc4f54","rdf:type")="sp:LabResult"
|
|---|
| 77 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:belongsTo")="smart:99912345"
|
|---|
| 78 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:labName")="qqWZZIew999"
|
|---|
| 79 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:narrativeResult")="qqWZZIew998"
|
|---|
| 80 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:specimenCollected")="qqWZZIew997"
|
|---|
| 81 | ;
|
|---|
| 82 | ;
|
|---|
| 83 | ; another Smart example, this one with sp:quantitativeResult
|
|---|
| 84 | ;
|
|---|
| 85 | ;G("loinc:786-4","dcterms:identifier")="786-4"
|
|---|
| 86 | ;G("loinc:786-4","dcterms:title")="MCHC RBC Auto-mCnc"
|
|---|
| 87 | ;G("loinc:786-4","rdf:type")="sp:Code"
|
|---|
| 88 | ;G("loinc:786-4","sp:system")="http://loinc.org/codes/"
|
|---|
| 89 | ;G("nodeID:4439","rdf:type")="sp:ValueAndUnit"
|
|---|
| 90 | ;G("nodeID:4439","sp:unit")="g/dL"
|
|---|
| 91 | ;G("nodeID:4439","sp:value")=36.6
|
|---|
| 92 | ;G("nodeID:4613","rdf:type")="sp:ValueAndUnit"
|
|---|
| 93 | ;G("nodeID:4613","sp:unit")="g/dL"
|
|---|
| 94 | ;G("nodeID:4613","sp:value")=32
|
|---|
| 95 | ;G("nodeID:4672","rdf:type")="sp:Attribution"
|
|---|
| 96 | ;G("nodeID:4672","sp:startDate")="2005-03-10"
|
|---|
| 97 | ;G("nodeID:4866","rdf:type")="sp:ValueAndUnit"
|
|---|
| 98 | ;G("nodeID:4866","sp:unit")="g/dL"
|
|---|
| 99 | ;G("nodeID:4866","sp:value")=36
|
|---|
| 100 | ;G("nodeID:4871","dcterms:title")="MCHC RBC Auto-mCnc"
|
|---|
| 101 | ;G("nodeID:4871","rdf:type")="sp:CodedValue"
|
|---|
| 102 | ;G("nodeID:4871","sp:code")="loinc:786-4"
|
|---|
| 103 | ;G("nodeID:5221","rdf:type")="sp:QuantitativeResult"
|
|---|
| 104 | ;G("nodeID:5221","sp:normalRange")="nodeID:5282"
|
|---|
| 105 | ;G("nodeID:5221","sp:valueAndUnit")="nodeID:4439"
|
|---|
| 106 | ;G("nodeID:5282","rdf:type")="sp:ValueRange"
|
|---|
| 107 | ;G("nodeID:5282","sp:maximum")="nodeID:4866"
|
|---|
| 108 | ;G("nodeID:5282","sp:minimum")="nodeID:4613"
|
|---|
| 109 | ;G("smart:1540505/lab_results/2fc100850766","rdf:type")="sp:LabResult"
|
|---|
| 110 | ;G("smart:1540505/lab_results/2fc100850766","sp:belongsTo")="smart:1540505"
|
|---|
| 111 | ;G("smart:1540505/lab_results/2fc100850766","sp:labName")="nodeID:4871"
|
|---|
| 112 | ;G("smart:1540505/lab_results/2fc100850766","sp:quantitativeResult")="nodeID:5221"
|
|---|
| 113 | ;G("smart:1540505/lab_results/2fc100850766","sp:specimenCollected")="nodeID:4672"
|
|---|
| 114 | ;
|
|---|
| 115 | LAB(GRTN,C0SARY) ; GRTN, passed by reference,
|
|---|
| 116 | ; is the return name of the graph created. "" if none
|
|---|
| 117 | ; C0SARY is passed in by reference and is the NHIN array of lab
|
|---|
| 118 | ;
|
|---|
| 119 | I $O(C0SARY("lab",""))="" D Q ;
|
|---|
| 120 | . I $D(DEBUG) W !,"No Labs"
|
|---|
| 121 | S GRTN="" ; default to no labs
|
|---|
| 122 | N C0SGRF
|
|---|
| 123 | S C0SGRF="vistaSmart:"_ZPATID_"/lab_results"
|
|---|
| 124 | I $D(DEBUG) W !,"Processing ",C0SGRF
|
|---|
| 125 | D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph
|
|---|
| 126 | D INITFARY^C0XF2N("C0XFARY") ; which triple store to use
|
|---|
| 127 | N FARY S FARY="C0XFARY"
|
|---|
| 128 | D USEFARY^C0XF2N(FARY)
|
|---|
| 129 | D VOCINIT^C0XUTIL
|
|---|
| 130 | ;
|
|---|
| 131 | D STARTADD^C0XF2N ; initialize to create triples
|
|---|
| 132 | ;
|
|---|
| 133 | N ZI S ZI=""
|
|---|
| 134 | F S ZI=$O(C0SARY("lab",ZI)) Q:ZI="" D ;
|
|---|
| 135 | . N LRN,ZR ; ZR is the local array for building the new triples
|
|---|
| 136 | . S LRN=$NA(C0SARY("lab",ZI)) ; base for values in this lab result
|
|---|
| 137 | . ;
|
|---|
| 138 | . N RSLTID ; unique Id for this lab result
|
|---|
| 139 | . S RSLTID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
|
|---|
| 140 | . ;
|
|---|
| 141 | . ; i don't like this because the same labs result gets a
|
|---|
| 142 | . ; different ID every time it's reported. Can't trace it back to VistA
|
|---|
| 143 | . ; I'd rather be using id@value ie "id@value")="CH;6889372.84;67003"
|
|---|
| 144 | . ; .. either that or store an OID with the lab result - but that
|
|---|
| 145 | . ; will have to wait for the redesign of file 60.. - gpl 4/16/2012
|
|---|
| 146 | . ;
|
|---|
| 147 | . N LOINC S LOINC=$G(@LRN@("loinc@value"))
|
|---|
| 148 | . I LOINC="" D Q ;
|
|---|
| 149 | . . I $D(DEBUG) W !,"NO LOINC VALUE, SKIPPING"
|
|---|
| 150 | . N LABTST S LABTST=$G(@LRN@("test@value"))
|
|---|
| 151 | . I $D(DEBUG) D ;
|
|---|
| 152 | . . W !,"Processing Lab Result ",RSLTID
|
|---|
| 153 | . . W !,"test: ",LABTST
|
|---|
| 154 | . . W !,"loinc: ",LOINC
|
|---|
| 155 | . ;
|
|---|
| 156 | . ; first do the base result graph
|
|---|
| 157 | . ;
|
|---|
| 158 | . S ZR("rdf:type")="sp:LabResult"
|
|---|
| 159 | . S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's lab results
|
|---|
| 160 | . ; ie /vista/smart/99912345/lab_results
|
|---|
| 161 | . ;
|
|---|
| 162 | . N LABNAME S LABNAME=$$ANONS^C0XF2N ; new node for lab name
|
|---|
| 163 | . S ZR("sp:labName")=LABNAME
|
|---|
| 164 | . ;
|
|---|
| 165 | . N NARRSLT S NARRSLT=$$ANONS^C0XF2N ; new node for narrative result
|
|---|
| 166 | . S ZR("sp:narrativeResult")=NARRSLT
|
|---|
| 167 | . ;
|
|---|
| 168 | . N QNTRSLT S QNTRSLT=$$ANONS^C0XF2N ; new node for narrative result
|
|---|
| 169 | . S ZR("sp:quantitativeResult")=QNTRSLT
|
|---|
| 170 | . ;
|
|---|
| 171 | . N SPECCOLL S SPECCOLL=$$ANONS^C0XF2N ; new node for specimen collected
|
|---|
| 172 | . S ZR("sp:specimenCollected")=SPECCOLL
|
|---|
| 173 | . ;
|
|---|
| 174 | . D ADDINN^C0XF2N(C0SGRF,RSLTID,.ZR) ; addIfNotNull the triples
|
|---|
| 175 | . K ZR ; clean up
|
|---|
| 176 | . ;
|
|---|
| 177 | . ; create the narrative result graph
|
|---|
| 178 | . ;
|
|---|
| 179 | . N IVAL S IVAL=$G(@LRN@("interpretation@value"))'="" D ; H OR L
|
|---|
| 180 | . I IVAL'=""
|
|---|
| 181 | . . S ZR("rdf:type")="sp:NarrativeResult"
|
|---|
| 182 | . . S ZR("sp:value")=$G(@LRN@("interpretation@value")) ; H or L
|
|---|
| 183 | . . I ZR("sp:value")="L" S ZR("sp:value")="abnormal"
|
|---|
| 184 | . . I ZR("sp:value")="H" S ZR("sp:value")="abnormal"
|
|---|
| 185 | . . I ZR("sp:value")="HH" S ZR("sp:value")="critical"
|
|---|
| 186 | . . I ZR("sp:value")="LL" S ZR("sp:value")="critical"
|
|---|
| 187 | . . D ADDINN^C0XF2N(C0SGRF,NARRSLT,.ZR)
|
|---|
| 188 | . . K ZR
|
|---|
| 189 | . ;
|
|---|
| 190 | . ; create the quantitative result graph
|
|---|
| 191 | . ;
|
|---|
| 192 | . S ZR("rdf:type")="sp:QuantitativeResult"
|
|---|
| 193 | . N NORMNM S NORMNM=$$ANONS^C0XF2N ; new node for normal range graph
|
|---|
| 194 | . N VUNM S VUNM=$$ANONS^C0XF2N ; new node for value and unit graph
|
|---|
| 195 | . N HASNORMAL S HASNORMAL=0
|
|---|
| 196 | . I $G(@LRN@("high@value"))'="" S HASNORMAL=1
|
|---|
| 197 | . I HASNORMAL S ZR("sp:normalRange")=NORMNM
|
|---|
| 198 | . S ZR("sp:valueAndUnit")=VUNM
|
|---|
| 199 | . D ADDINN^C0XF2N(C0SGRF,QNTRSLT,.ZR)
|
|---|
| 200 | . K ZR
|
|---|
| 201 | . ;
|
|---|
| 202 | . ; create the normal range graph
|
|---|
| 203 | . ;
|
|---|
| 204 | . I HASNORMAL D ;
|
|---|
| 205 | . . S ZR("rdf:type")="sp:ValueRange"
|
|---|
| 206 | . . N MAXNM S MAXNM=$$ANONS^C0XF2N ; new node for maximum graph
|
|---|
| 207 | . . N MINNM S MINNM=$$ANONS^C0XF2N ; new node for minimum graph
|
|---|
| 208 | . . S ZR("sp:maximum")=MAXNM
|
|---|
| 209 | . . S ZR("sp:minimum")=MINNM
|
|---|
| 210 | . . D ADDINN^C0XF2N(C0SGRF,NORMNM,.ZR)
|
|---|
| 211 | . . K ZR
|
|---|
| 212 | . . ;
|
|---|
| 213 | . . ; create the maximum graph
|
|---|
| 214 | . . ;
|
|---|
| 215 | . . S ZR("rdf:type")="sp:ValueAndUnit"
|
|---|
| 216 | . . S ZR("sp:unit")=$G(@LRN@("units@value"))
|
|---|
| 217 | . . S ZR("sp:value")=$G(@LRN@("high@value"))
|
|---|
| 218 | . . D ADDINN^C0XF2N(C0SGRF,MAXNM,.ZR)
|
|---|
| 219 | . . K ZR
|
|---|
| 220 | . . ;
|
|---|
| 221 | . . ; create the minimum graph
|
|---|
| 222 | . . ;
|
|---|
| 223 | . . S ZR("rdf:type")="sp:ValueAndUnit"
|
|---|
| 224 | . . S ZR("sp:unit")=$G(@LRN@("units@value"))
|
|---|
| 225 | . . S ZR("sp:value")=$G(@LRN@("low@value"))
|
|---|
| 226 | . . D ADDINN^C0XF2N(C0SGRF,MINNM,.ZR)
|
|---|
| 227 | . . K ZR
|
|---|
| 228 | . ;
|
|---|
| 229 | . ; create the value and unit graph
|
|---|
| 230 | . ;
|
|---|
| 231 | . S ZR("rdf:type")="sp:ValueAndUnit"
|
|---|
| 232 | . S ZR("sp:unit")=$G(@LRN@("units@value"))
|
|---|
| 233 | . I ZR("sp:unit")="" S ZR("sp:unit")="{unknown}" ; was $G(@LRN@("test@value")) gpl
|
|---|
| 234 | . S ZR("sp:value")=$G(@LRN@("result@value"))
|
|---|
| 235 | . D ADDINN^C0XF2N(C0SGRF,VUNM,.ZR)
|
|---|
| 236 | . K ZR
|
|---|
| 237 | . ;
|
|---|
| 238 | . ; create specimen collected graph
|
|---|
| 239 | . ;
|
|---|
| 240 | . S ZR("rdf:type")="sp:Attribution"
|
|---|
| 241 | . S ZR("sp:startDate")=$$SPDATE^C0SUTIL($G(@LRN@("collected@value")))
|
|---|
| 242 | . D ADDINN^C0XF2N(C0SGRF,SPECCOLL,.ZR)
|
|---|
| 243 | . K ZR
|
|---|
| 244 | . ;
|
|---|
| 245 | . ; create lab name graph - this contains the test name and code
|
|---|
| 246 | . ;
|
|---|
| 247 | . I LOINC'="" D ;
|
|---|
| 248 | . . S ZR("rdf:type")="sp:CodedValue"
|
|---|
| 249 | . . S ZR("dcterms:title")=LABTST
|
|---|
| 250 | . . N LOINCNM S LOINCNM="loinc:"_LOINC
|
|---|
| 251 | . . S ZR("sp:code")="loinc:"_LOINC
|
|---|
| 252 | . . D ADDINN^C0XF2N(C0SGRF,LABNAME,.ZR)
|
|---|
| 253 | . . K ZR
|
|---|
| 254 | . . S ZR("dcterms:identifier")=LOINC
|
|---|
| 255 | . . S ZR("dcterms:title")=LABTST
|
|---|
| 256 | . . S ZR("rdf:type")="sp:Code"
|
|---|
| 257 | . . S ZR("sp:system")="http://loinc.org/codes/"
|
|---|
| 258 | . . D ADDINN^C0XF2N(C0SGRF,LOINCNM,.ZR)
|
|---|
| 259 | . . K ZR
|
|---|
| 260 | . ;
|
|---|
| 261 | . ; that's all for now folks (there is more to do like reference ranges
|
|---|
| 262 | . ; and result values)
|
|---|
| 263 | . ;
|
|---|
| 264 | D BULKLOAD^C0XF2N(.C0XFDA)
|
|---|
| 265 | S GRTN=C0SGRF
|
|---|
| 266 | Q
|
|---|
| 267 | ;
|
|---|
| 268 | SAMPLE ; import sample lab tests to the triplestore
|
|---|
| 269 | N GN
|
|---|
| 270 | S GN=$NA(^rdf("lab_results"))
|
|---|
| 271 | D INSRDF^C0XF2N(GN,"/smart/lab/samples")
|
|---|
| 272 | Q
|
|---|
| 273 | ;
|
|---|
