| [1526] | 1 | C0SLAB ; GPL - Smart Lab Processing ;4/15/12 17:05
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| 2 | ;;0.1;C0S;nopatch;noreleasedate;Build 2
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| 3 | ;Copyright 2012 George Lilly. Licensed under the terms of the GNU
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| 4 | ;General Public License See attached copy of the License.
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| 5 | ;
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| 6 | ;This program is free software; you can redistribute it and/or modify
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| 7 | ;it under the terms of the GNU General Public License as published by
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| 8 | ;the Free Software Foundation; either version 2 of the License, or
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| 9 | ;(at your option) any later version.
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| 10 | ;
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| 11 | ;This program is distributed in the hope that it will be useful,
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| 12 | ;but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 13 | ;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 14 | ;GNU General Public License for more details.
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| 15 | ;
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| 16 | ;You should have received a copy of the GNU General Public License along
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| 17 | ;with this program; if not, write to the Free Software Foundation, Inc.,
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| 18 | ;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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| 19 | ;
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| 20 | Q
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| 21 | ;
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| 22 | ; sample VistA NHIN lab result
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| 23 | ;
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| 24 | ;^TMP("C0STBL",32,"lab",8,"collected@value")=3110626.16
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| 25 | ;^TMP("C0STBL",32,"lab",8,"comment")="Report Released Date/Time: Jun 26, 2011@19:00"
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| 26 | ;^TMP("C0STBL",32,"lab",8,"comment@xml:space")="preserve"
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| 27 | ;^TMP("C0STBL",32,"lab",8,"facility@code")=100
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| 28 | ;^TMP("C0STBL",32,"lab",8,"facility@name")="VOE OFFICE INSTITUTION"
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| 29 | ;^TMP("C0STBL",32,"lab",8,"groupName@value")="CH 0626 47"
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| 30 | ;^TMP("C0STBL",32,"lab",8,"high@value")=" 101"
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| 31 | ;^TMP("C0STBL",32,"lab",8,"id@value")="CH;6889372.84;67003"
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| 32 | ;^TMP("C0STBL",32,"lab",8,"interpretation@value")="H"
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| 33 | ;^TMP("C0STBL",32,"lab",8,"labOrderID@value")=336
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| 34 | ;^TMP("C0STBL",32,"lab",8,"localName@value")="FBLDGLU"
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| 35 | ;^TMP("C0STBL",32,"lab",8,"loinc@value")="14771-0"
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| 36 | ;^TMP("C0STBL",32,"lab",8,"low@value")="69 "
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| 37 | ;^TMP("C0STBL",32,"lab",8,"orderID@value")=807
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| 38 | ;^TMP("C0STBL",32,"lab",8,"result@value")=178
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| 39 | ;^TMP("C0STBL",32,"lab",8,"resulted@value")=3110626.190006
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| 40 | ;^TMP("C0STBL",32,"lab",8,"sample@value")="SERUM"
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| 41 | ;^TMP("C0STBL",32,"lab",8,"specimen@code")="0X500"
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| 42 | ;^TMP("C0STBL",32,"lab",8,"specimen@name")="SERUM"
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| 43 | ;^TMP("C0STBL",32,"lab",8,"status@value")="completed"
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| 44 | ;^TMP("C0STBL",32,"lab",8,"test@value")="FASTING BLOOD GLUCOSE"
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| 45 | ;^TMP("C0STBL",32,"lab",8,"type@value")="CH"
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| 46 | ;^TMP("C0STBL",32,"lab",8,"units@value")="MG/DL"
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| 47 | ;^TMP("C0STBL",32,"lab",8,"vuid@value")=4656342
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| 48 | ;
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| 49 | ; sample Smart lab result triples
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| 50 | ;
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| 51 | ;G("loinc:29571-7","dcterms:identifier")="29571-7"
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| 52 | ;G("loinc:29571-7","dcterms:title")="Phe DBS Ql"
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| 53 | ;G("loinc:29571-7","rdf:type")="sp:Code"
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| 54 | ;G("loinc:29571-7","sp:system")="http://loinc.org/codes/"
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| 55 | ;G("loinc:38478-4","dcterms:identifier")="38478-4"
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| 56 | ;G("loinc:38478-4","dcterms:title")="Biotinidase DBS Ql"
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| 57 | ;G("loinc:38478-4","rdf:type")="sp:Code"
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| 58 | ;G("loinc:38478-4","sp:system")="http://loinc.org/codes/"
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| 59 | ;G("qqWZZIew993","rdf:type")="sp:Attribution"
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| 60 | ;G("qqWZZIew993","sp:startDate")="2007-04-21"
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| 61 | ;G("qqWZZIew994","rdf:type")="sp:NarrativeResult"
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| 62 | ;G("qqWZZIew994","sp:value")="Normal"
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| 63 | ;G("qqWZZIew995","dcterms:title")="Biotinidase DBS Ql"
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| 64 | ;G("qqWZZIew995","rdf:type")="sp:CodedValue"
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| 65 | ;G("qqWZZIew995","sp:code")="loinc:38478-4"
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| 66 | ;G("qqWZZIew997","rdf:type")="sp:Attribution"
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| 67 | ;G("qqWZZIew997","sp:startDate")="2007-09-08"
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| 68 | ;G("qqWZZIew998","rdf:type")="sp:NarrativeResult"
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| 69 | ;G("qqWZZIew998","sp:value")="Normal"
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| 70 | ;G("qqWZZIew999","dcterms:title")="Phe DBS Ql"
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| 71 | ;G("qqWZZIew999","rdf:type")="sp:CodedValue"
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| 72 | ;G("qqWZZIew999","sp:code")="loinc:29571-7"
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| 73 | ;G("smart:99912345/lab_results/3d9b39249193","rdf:type")="sp:LabResult"
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| 74 | ;G("smart:99912345/lab_results/3d9b39249193","sp:belongsTo")="smart:99912345"
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| 75 | ;G("smart:99912345/lab_results/3d9b39249193","sp:labName")="qqWZZIew995"
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| 76 | ;G("smart:99912345/lab_results/3d9b39249193","sp:narrativeResult")="qqWZZIew994"
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| 77 | ;G("smart:99912345/lab_results/3d9b39249193","sp:specimenCollected")="qqWZZIew993"
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| 78 | ;G("smart:99912345/lab_results/426c7adc4f54","rdf:type")="sp:LabResult"
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| 79 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:belongsTo")="smart:99912345"
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| 80 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:labName")="qqWZZIew999"
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| 81 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:narrativeResult")="qqWZZIew998"
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| 82 | ;G("smart:99912345/lab_results/426c7adc4f54","sp:specimenCollected")="qqWZZIew997"
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| 83 | ;
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| 84 | ;
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| 85 | ; another Smart example, this one with sp:quantitativeResult
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| 86 | ;
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| 87 | ;G("loinc:786-4","dcterms:identifier")="786-4"
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| 88 | ;G("loinc:786-4","dcterms:title")="MCHC RBC Auto-mCnc"
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| 89 | ;G("loinc:786-4","rdf:type")="sp:Code"
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| 90 | ;G("loinc:786-4","sp:system")="http://loinc.org/codes/"
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| 91 | ;G("nodeID:4439","rdf:type")="sp:ValueAndUnit"
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| 92 | ;G("nodeID:4439","sp:unit")="g/dL"
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| 93 | ;G("nodeID:4439","sp:value")=36.6
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| 94 | ;G("nodeID:4613","rdf:type")="sp:ValueAndUnit"
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| 95 | ;G("nodeID:4613","sp:unit")="g/dL"
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| 96 | ;G("nodeID:4613","sp:value")=32
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| 97 | ;G("nodeID:4672","rdf:type")="sp:Attribution"
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| 98 | ;G("nodeID:4672","sp:startDate")="2005-03-10"
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| 99 | ;G("nodeID:4866","rdf:type")="sp:ValueAndUnit"
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| 100 | ;G("nodeID:4866","sp:unit")="g/dL"
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| 101 | ;G("nodeID:4866","sp:value")=36
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| 102 | ;G("nodeID:4871","dcterms:title")="MCHC RBC Auto-mCnc"
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| 103 | ;G("nodeID:4871","rdf:type")="sp:CodedValue"
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| 104 | ;G("nodeID:4871","sp:code")="loinc:786-4"
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| 105 | ;G("nodeID:5221","rdf:type")="sp:QuantitativeResult"
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| 106 | ;G("nodeID:5221","sp:normalRange")="nodeID:5282"
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| 107 | ;G("nodeID:5221","sp:valueAndUnit")="nodeID:4439"
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| 108 | ;G("nodeID:5282","rdf:type")="sp:ValueRange"
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| 109 | ;G("nodeID:5282","sp:maximum")="nodeID:4866"
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| 110 | ;G("nodeID:5282","sp:minimum")="nodeID:4613"
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| 111 | ;G("smart:1540505/lab_results/2fc100850766","rdf:type")="sp:LabResult"
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| 112 | ;G("smart:1540505/lab_results/2fc100850766","sp:belongsTo")="smart:1540505"
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| 113 | ;G("smart:1540505/lab_results/2fc100850766","sp:labName")="nodeID:4871"
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| 114 | ;G("smart:1540505/lab_results/2fc100850766","sp:quantitativeResult")="nodeID:5221"
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| 115 | ;G("smart:1540505/lab_results/2fc100850766","sp:specimenCollected")="nodeID:4672"
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| 116 | ;
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| 117 | LAB(GRTN,C0SARY) ; GRTN, passed by reference,
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| 118 | ; is the return name of the graph created. "" if none
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| 119 | ; C0SARY is passed in by reference and is the NHIN array of lab
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| 120 | ;
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| 121 | I $O(C0SARY("lab",""))="" D Q ;
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| 122 | . I $D(DEBUG) W !,"No Labs"
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| 123 | S GRTN="" ; default to no labs
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| 124 | N C0SGRF
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| 125 | S C0SGRF="vistaSmart:"_ZPATID_"/lab_results"
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| 126 | I $D(DEBUG) W !,"Processing ",C0SGRF
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| 127 | D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph
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| 128 | D INITFARY^C0XF2N("C0XFARY") ; which triple store to use
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| 129 | N FARY S FARY="C0XFARY"
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| 130 | D USEFARY^C0XF2N(FARY)
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| 131 | D VOCINIT^C0XUTIL
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| 132 | ;
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| 133 | D STARTADD^C0XF2N ; initialize to create triples
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| 134 | ;
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| 135 | N ZI S ZI=""
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| 136 | F S ZI=$O(C0SARY("lab",ZI)) Q:ZI="" D ;
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| 137 | . N LRN,ZR ; ZR is the local array for building the new triples
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| 138 | . S LRN=$NA(C0SARY("lab",ZI)) ; base for values in this lab result
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| 139 | . ;
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| 140 | . N RSLTID ; unique Id for this lab result
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| 141 | . S RSLTID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
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| 142 | . ;
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| 143 | . ; i don't like this because the same labs result gets a
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| 144 | . ; different ID every time it's reported. Can't trace it back to VistA
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| 145 | . ; I'd rather be using id@value ie "id@value")="CH;6889372.84;67003"
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| 146 | . ; .. either that or store an OID with the lab result - but that
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| 147 | . ; will have to wait for the redesign of file 60.. - gpl 4/16/2012
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| 148 | . ;
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| 149 | . N LOINC S LOINC=$G(@LRN@("loinc@value"))
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| 150 | . I LOINC="" D Q ;
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| 151 | . . I $D(DEBUG) W !,"NO LOINC VALUE, SKIPPING"
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| 152 | . N LABTST S LABTST=$G(@LRN@("test@value"))
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| 153 | . I $D(DEBUG) D ;
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| 154 | . . W !,"Processing Lab Result ",RSLTID
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| 155 | . . W !,"test: ",LABTST
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| 156 | . . W !,"loinc: ",LOINC
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| 157 | . ;
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| 158 | . ; first do the base result graph
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| 159 | . ;
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| 160 | . S ZR("rdf:type")="sp:LabResult"
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| 161 | . S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's lab results
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| 162 | . ; ie /vista/smart/99912345/lab_results
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| 163 | . ;
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| 164 | . N LABNAME S LABNAME=$$ANONS^C0XF2N ; new node for lab name
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| 165 | . S ZR("sp:labName")=LABNAME
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| 166 | . ;
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| 167 | . N NARRSLT S NARRSLT=$$ANONS^C0XF2N ; new node for narrative result
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| 168 | . S ZR("sp:narrativeResult")=NARRSLT
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| 169 | . ;
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| 170 | . N QNTRSLT S QNTRSLT=$$ANONS^C0XF2N ; new node for narrative result
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| 171 | . S ZR("sp:quantitativeResult")=QNTRSLT
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| 172 | . ;
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| 173 | . N SPECCOLL S SPECCOLL=$$ANONS^C0XF2N ; new node for specimen collected
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| 174 | . S ZR("sp:specimenCollected")=SPECCOLL
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| 175 | . ;
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| 176 | . D ADDINN^C0XF2N(C0SGRF,RSLTID,.ZR) ; addIfNotNull the triples
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| 177 | . K ZR ; clean up
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| 178 | . ;
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| 179 | . ; create the narrative result graph
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| 180 | . ;
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| 181 | . N IVAL S IVAL=$G(@LRN@("interpretation@value"))'="" D ; H OR L
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| 182 | . I IVAL'=""
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| 183 | . . S ZR("rdf:type")="sp:NarrativeResult"
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| 184 | . . S ZR("sp:value")=$G(@LRN@("interpretation@value")) ; H or L
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| 185 | . . I ZR("sp:value")="L" S ZR("sp:value")="abnormal"
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| 186 | . . I ZR("sp:value")="H" S ZR("sp:value")="abnormal"
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| 187 | . . I ZR("sp:value")="HH" S ZR("sp:value")="critical"
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| 188 | . . I ZR("sp:value")="LL" S ZR("sp:value")="critical"
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| 189 | . . D ADDINN^C0XF2N(C0SGRF,NARRSLT,.ZR)
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| 190 | . . K ZR
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| 191 | . ;
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| 192 | . ; create the quantitative result graph
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| 193 | . ;
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| 194 | . S ZR("rdf:type")="sp:QuantitativeResult"
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| 195 | . N NORMNM S NORMNM=$$ANONS^C0XF2N ; new node for normal range graph
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| 196 | . N VUNM S VUNM=$$ANONS^C0XF2N ; new node for value and unit graph
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| 197 | . N HASNORMAL S HASNORMAL=0
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| 198 | . I $G(@LRN@("high@value"))'="" S HASNORMAL=1
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| 199 | . I HASNORMAL S ZR("sp:normalRange")=NORMNM
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| 200 | . S ZR("sp:valueAndUnit")=VUNM
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| 201 | . D ADDINN^C0XF2N(C0SGRF,QNTRSLT,.ZR)
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| 202 | . K ZR
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| 203 | . ;
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| 204 | . ; create the normal range graph
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| 205 | . ;
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| 206 | . I HASNORMAL D ;
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| 207 | . . S ZR("rdf:type")="sp:ValueRange"
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| 208 | . . N MAXNM S MAXNM=$$ANONS^C0XF2N ; new node for maximum graph
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| 209 | . . N MINNM S MINNM=$$ANONS^C0XF2N ; new node for minimum graph
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| 210 | . . S ZR("sp:maximum")=MAXNM
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| 211 | . . S ZR("sp:minimum")=MINNM
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| 212 | . . D ADDINN^C0XF2N(C0SGRF,NORMNM,.ZR)
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| 213 | . . K ZR
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| 214 | . . ;
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| 215 | . . ; create the maximum graph
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| 216 | . . ;
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| 217 | . . S ZR("rdf:type")="sp:ValueAndUnit"
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| 218 | . . S ZR("sp:unit")=$G(@LRN@("units@value"))
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| 219 | . . S ZR("sp:value")=$G(@LRN@("high@value"))
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| 220 | . . D ADDINN^C0XF2N(C0SGRF,MAXNM,.ZR)
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| 221 | . . K ZR
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| 222 | . . ;
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| 223 | . . ; create the minimum graph
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| 224 | . . ;
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| 225 | . . S ZR("rdf:type")="sp:ValueAndUnit"
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| 226 | . . S ZR("sp:unit")=$G(@LRN@("units@value"))
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| 227 | . . S ZR("sp:value")=$G(@LRN@("low@value"))
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| 228 | . . D ADDINN^C0XF2N(C0SGRF,MINNM,.ZR)
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| 229 | . . K ZR
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| 230 | . ;
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| 231 | . ; create the value and unit graph
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| 232 | . ;
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| 233 | . S ZR("rdf:type")="sp:ValueAndUnit"
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| 234 | . S ZR("sp:unit")=$G(@LRN@("units@value"))
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| 235 | . I ZR("sp:unit")="" S ZR("sp:unit")=$G(@LRN@("test@value"))
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| 236 | . S ZR("sp:value")=$G(@LRN@("result@value"))
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| 237 | . D ADDINN^C0XF2N(C0SGRF,VUNM,.ZR)
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| 238 | . K ZR
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| 239 | . ;
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| 240 | . ; create specimen collected graph
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| 241 | . ;
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| 242 | . S ZR("rdf:type")="sp:Attribution"
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| 243 | . S ZR("sp:startDate")=$$SPDATE^C0SUTIL($G(@LRN@("collected@value")))
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| 244 | . D ADDINN^C0XF2N(C0SGRF,SPECCOLL,.ZR)
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| 245 | . K ZR
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| 246 | . ;
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| 247 | . ; create lab name graph - this contains the test name and code
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| 248 | . ;
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| 249 | . I LOINC'="" D ;
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| 250 | . . S ZR("rdf:type")="sp:CodedValue"
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| 251 | . . S ZR("dcterms:title")=LABTST
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| 252 | . . N LOINCNM S LOINCNM="loinc:"_LOINC
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| 253 | . . S ZR("sp:code")="loinc:"_LOINC
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| 254 | . . D ADDINN^C0XF2N(C0SGRF,LABNAME,.ZR)
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| 255 | . . K ZR
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| 256 | . . S ZR("dcterms:identifier")=LOINC
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| 257 | . . S ZR("dcterms:title")=LABTST
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| 258 | . . S ZR("rdf:type")="sp:Code"
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| 259 | . . S ZR("sp:system")="http://loinc.org/codes/"
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| 260 | . . D ADDINN^C0XF2N(C0SGRF,LOINCNM,.ZR)
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| 261 | . . K ZR
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| 262 | . ;
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| 263 | . ; that's all for now folks (there is more to do like reference ranges
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| 264 | . ; and result values)
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| 265 | . ;
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| 266 | D BULKLOAD^C0XF2N(.C0XFDA)
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| 267 | S GRTN=C0SGRF
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| 268 | Q
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| 269 | ;
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| 270 | SAMPLE ; import sample lab tests to the triplestore
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| 271 | N GN
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| 272 | S GN=$NA(^rdf("lab_results"))
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| 273 | D INSRDF^C0XF2N(GN,"/smart/lab/samples")
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| 274 | Q
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| 275 | ; |
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