2012-10-13 14:49:26 -04:00
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C0SLAB ; GPL - Smart Lab Processing ;4/15/12 17:05
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2012-10-30 13:53:46 -04:00
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;;1.0;VISTA SMART CONTAINER;;Sep 26, 2012;Build 5
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;Copyright 2012 George Lilly.
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2012-10-13 14:49:26 -04:00
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;
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2012-10-30 13:53:46 -04:00
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; This program is free software: you can redistribute it and/or modify
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; it under the terms of the GNU Affero General Public License as
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; published by the Free Software Foundation, either version 3 of the
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; License, or (at your option) any later version.
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2012-10-13 14:49:26 -04:00
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;
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2012-10-30 13:53:46 -04:00
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; This program is distributed in the hope that it will be useful,
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; but WITHOUT ANY WARRANTY; without even the implied warranty of
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; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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; GNU Affero General Public License for more details.
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2012-10-13 14:49:26 -04:00
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;
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2012-10-30 13:53:46 -04:00
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; You should have received a copy of the GNU Affero General Public License
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; along with this program. If not, see <http://www.gnu.org/licenses/>.
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2012-10-13 14:49:26 -04:00
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;
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Q
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;
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; sample VistA NHIN lab result
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;
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;^TMP("C0STBL",32,"lab",8,"collected@value")=3110626.16
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;^TMP("C0STBL",32,"lab",8,"comment")="Report Released Date/Time: Jun 26, 2011@19:00"
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;^TMP("C0STBL",32,"lab",8,"comment@xml:space")="preserve"
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;^TMP("C0STBL",32,"lab",8,"facility@code")=100
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;^TMP("C0STBL",32,"lab",8,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",32,"lab",8,"groupName@value")="CH 0626 47"
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;^TMP("C0STBL",32,"lab",8,"high@value")=" 101"
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;^TMP("C0STBL",32,"lab",8,"id@value")="CH;6889372.84;67003"
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;^TMP("C0STBL",32,"lab",8,"interpretation@value")="H"
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;^TMP("C0STBL",32,"lab",8,"labOrderID@value")=336
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;^TMP("C0STBL",32,"lab",8,"localName@value")="FBLDGLU"
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;^TMP("C0STBL",32,"lab",8,"loinc@value")="14771-0"
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;^TMP("C0STBL",32,"lab",8,"low@value")="69 "
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;^TMP("C0STBL",32,"lab",8,"orderID@value")=807
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;^TMP("C0STBL",32,"lab",8,"result@value")=178
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;^TMP("C0STBL",32,"lab",8,"resulted@value")=3110626.190006
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;^TMP("C0STBL",32,"lab",8,"sample@value")="SERUM"
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;^TMP("C0STBL",32,"lab",8,"specimen@code")="0X500"
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;^TMP("C0STBL",32,"lab",8,"specimen@name")="SERUM"
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;^TMP("C0STBL",32,"lab",8,"status@value")="completed"
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;^TMP("C0STBL",32,"lab",8,"test@value")="FASTING BLOOD GLUCOSE"
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;^TMP("C0STBL",32,"lab",8,"type@value")="CH"
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;^TMP("C0STBL",32,"lab",8,"units@value")="MG/DL"
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;^TMP("C0STBL",32,"lab",8,"vuid@value")=4656342
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;
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; sample Smart lab result triples
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;
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;G("loinc:29571-7","dcterms:identifier")="29571-7"
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;G("loinc:29571-7","dcterms:title")="Phe DBS Ql"
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;G("loinc:29571-7","rdf:type")="sp:Code"
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;G("loinc:29571-7","sp:system")="http://loinc.org/codes/"
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;G("loinc:38478-4","dcterms:identifier")="38478-4"
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;G("loinc:38478-4","dcterms:title")="Biotinidase DBS Ql"
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;G("loinc:38478-4","rdf:type")="sp:Code"
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;G("loinc:38478-4","sp:system")="http://loinc.org/codes/"
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;G("qqWZZIew993","rdf:type")="sp:Attribution"
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;G("qqWZZIew993","sp:startDate")="2007-04-21"
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;G("qqWZZIew994","rdf:type")="sp:NarrativeResult"
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;G("qqWZZIew994","sp:value")="Normal"
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;G("qqWZZIew995","dcterms:title")="Biotinidase DBS Ql"
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;G("qqWZZIew995","rdf:type")="sp:CodedValue"
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;G("qqWZZIew995","sp:code")="loinc:38478-4"
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;G("qqWZZIew997","rdf:type")="sp:Attribution"
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;G("qqWZZIew997","sp:startDate")="2007-09-08"
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;G("qqWZZIew998","rdf:type")="sp:NarrativeResult"
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;G("qqWZZIew998","sp:value")="Normal"
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;G("qqWZZIew999","dcterms:title")="Phe DBS Ql"
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;G("qqWZZIew999","rdf:type")="sp:CodedValue"
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;G("qqWZZIew999","sp:code")="loinc:29571-7"
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;G("smart:99912345/lab_results/3d9b39249193","rdf:type")="sp:LabResult"
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;G("smart:99912345/lab_results/3d9b39249193","sp:belongsTo")="smart:99912345"
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;G("smart:99912345/lab_results/3d9b39249193","sp:labName")="qqWZZIew995"
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;G("smart:99912345/lab_results/3d9b39249193","sp:narrativeResult")="qqWZZIew994"
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;G("smart:99912345/lab_results/3d9b39249193","sp:specimenCollected")="qqWZZIew993"
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;G("smart:99912345/lab_results/426c7adc4f54","rdf:type")="sp:LabResult"
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;G("smart:99912345/lab_results/426c7adc4f54","sp:belongsTo")="smart:99912345"
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;G("smart:99912345/lab_results/426c7adc4f54","sp:labName")="qqWZZIew999"
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;G("smart:99912345/lab_results/426c7adc4f54","sp:narrativeResult")="qqWZZIew998"
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;G("smart:99912345/lab_results/426c7adc4f54","sp:specimenCollected")="qqWZZIew997"
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;
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;
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; another Smart example, this one with sp:quantitativeResult
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;
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;G("loinc:786-4","dcterms:identifier")="786-4"
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;G("loinc:786-4","dcterms:title")="MCHC RBC Auto-mCnc"
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;G("loinc:786-4","rdf:type")="sp:Code"
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;G("loinc:786-4","sp:system")="http://loinc.org/codes/"
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;G("nodeID:4439","rdf:type")="sp:ValueAndUnit"
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;G("nodeID:4439","sp:unit")="g/dL"
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;G("nodeID:4439","sp:value")=36.6
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;G("nodeID:4613","rdf:type")="sp:ValueAndUnit"
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;G("nodeID:4613","sp:unit")="g/dL"
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;G("nodeID:4613","sp:value")=32
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;G("nodeID:4672","rdf:type")="sp:Attribution"
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;G("nodeID:4672","sp:startDate")="2005-03-10"
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;G("nodeID:4866","rdf:type")="sp:ValueAndUnit"
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;G("nodeID:4866","sp:unit")="g/dL"
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;G("nodeID:4866","sp:value")=36
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;G("nodeID:4871","dcterms:title")="MCHC RBC Auto-mCnc"
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;G("nodeID:4871","rdf:type")="sp:CodedValue"
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;G("nodeID:4871","sp:code")="loinc:786-4"
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;G("nodeID:5221","rdf:type")="sp:QuantitativeResult"
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;G("nodeID:5221","sp:normalRange")="nodeID:5282"
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;G("nodeID:5221","sp:valueAndUnit")="nodeID:4439"
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;G("nodeID:5282","rdf:type")="sp:ValueRange"
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;G("nodeID:5282","sp:maximum")="nodeID:4866"
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;G("nodeID:5282","sp:minimum")="nodeID:4613"
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;G("smart:1540505/lab_results/2fc100850766","rdf:type")="sp:LabResult"
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;G("smart:1540505/lab_results/2fc100850766","sp:belongsTo")="smart:1540505"
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;G("smart:1540505/lab_results/2fc100850766","sp:labName")="nodeID:4871"
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;G("smart:1540505/lab_results/2fc100850766","sp:quantitativeResult")="nodeID:5221"
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;G("smart:1540505/lab_results/2fc100850766","sp:specimenCollected")="nodeID:4672"
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;
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LAB(GRTN,C0SARY) ; GRTN, passed by reference,
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; is the return name of the graph created. "" if none
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; C0SARY is passed in by reference and is the NHIN array of lab
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;
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I $O(C0SARY("lab",""))="" D Q ;
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. I $D(DEBUG) W !,"No Labs"
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S GRTN="" ; default to no labs
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N C0SGRF
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S C0SGRF="vistaSmart:"_ZPATID_"/lab_results"
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I $D(DEBUG) W !,"Processing ",C0SGRF
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D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph
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D INITFARY^C0XF2N("C0XFARY") ; which triple store to use
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N FARY S FARY="C0XFARY"
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D USEFARY^C0XF2N(FARY)
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D VOCINIT^C0XUTIL
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;
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D STARTADD^C0XF2N ; initialize to create triples
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;
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N ZI S ZI=""
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F S ZI=$O(C0SARY("lab",ZI)) Q:ZI="" D ;
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. N LRN,ZR ; ZR is the local array for building the new triples
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. S LRN=$NA(C0SARY("lab",ZI)) ; base for values in this lab result
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. ;
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. N RSLTID ; unique Id for this lab result
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. S RSLTID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
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. ;
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. ; i don't like this because the same labs result gets a
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. ; different ID every time it's reported. Can't trace it back to VistA
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. ; I'd rather be using id@value ie "id@value")="CH;6889372.84;67003"
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. ; .. either that or store an OID with the lab result - but that
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. ; will have to wait for the redesign of file 60.. - gpl 4/16/2012
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. ;
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. N LOINC S LOINC=$G(@LRN@("loinc@value"))
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. I LOINC="" D Q ;
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. . I $D(DEBUG) W !,"NO LOINC VALUE, SKIPPING"
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. N LABTST S LABTST=$G(@LRN@("test@value"))
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. I $D(DEBUG) D ;
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. . W !,"Processing Lab Result ",RSLTID
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. . W !,"test: ",LABTST
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. . W !,"loinc: ",LOINC
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. ;
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. ; first do the base result graph
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. ;
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. S ZR("rdf:type")="sp:LabResult"
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. S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's lab results
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. ; ie /vista/smart/99912345/lab_results
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. ;
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. N LABNAME S LABNAME=$$ANONS^C0XF2N ; new node for lab name
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. S ZR("sp:labName")=LABNAME
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. ;
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. N NARRSLT S NARRSLT=$$ANONS^C0XF2N ; new node for narrative result
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. S ZR("sp:narrativeResult")=NARRSLT
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. ;
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. N QNTRSLT S QNTRSLT=$$ANONS^C0XF2N ; new node for narrative result
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. S ZR("sp:quantitativeResult")=QNTRSLT
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. ;
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. N SPECCOLL S SPECCOLL=$$ANONS^C0XF2N ; new node for specimen collected
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. S ZR("sp:specimenCollected")=SPECCOLL
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. ;
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. D ADDINN^C0XF2N(C0SGRF,RSLTID,.ZR) ; addIfNotNull the triples
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. K ZR ; clean up
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. ;
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. ; create the narrative result graph
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. ;
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. N IVAL S IVAL=$G(@LRN@("interpretation@value"))'="" D ; H OR L
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. I IVAL'=""
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. . S ZR("rdf:type")="sp:NarrativeResult"
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. . S ZR("sp:value")=$G(@LRN@("interpretation@value")) ; H or L
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. . I ZR("sp:value")="L" S ZR("sp:value")="abnormal"
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. . I ZR("sp:value")="H" S ZR("sp:value")="abnormal"
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. . I ZR("sp:value")="HH" S ZR("sp:value")="critical"
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. . I ZR("sp:value")="LL" S ZR("sp:value")="critical"
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. . D ADDINN^C0XF2N(C0SGRF,NARRSLT,.ZR)
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. . K ZR
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. ;
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. ; create the quantitative result graph
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. ;
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. S ZR("rdf:type")="sp:QuantitativeResult"
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. N NORMNM S NORMNM=$$ANONS^C0XF2N ; new node for normal range graph
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. N VUNM S VUNM=$$ANONS^C0XF2N ; new node for value and unit graph
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. N HASNORMAL S HASNORMAL=0
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. I $G(@LRN@("high@value"))'="" S HASNORMAL=1
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. I HASNORMAL S ZR("sp:normalRange")=NORMNM
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. S ZR("sp:valueAndUnit")=VUNM
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. D ADDINN^C0XF2N(C0SGRF,QNTRSLT,.ZR)
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. K ZR
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. ;
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. ; create the normal range graph
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. ;
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. I HASNORMAL D ;
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. . S ZR("rdf:type")="sp:ValueRange"
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. . N MAXNM S MAXNM=$$ANONS^C0XF2N ; new node for maximum graph
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. . N MINNM S MINNM=$$ANONS^C0XF2N ; new node for minimum graph
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. . S ZR("sp:maximum")=MAXNM
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. . S ZR("sp:minimum")=MINNM
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. . D ADDINN^C0XF2N(C0SGRF,NORMNM,.ZR)
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. . K ZR
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. . ;
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. . ; create the maximum graph
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. . ;
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. . S ZR("rdf:type")="sp:ValueAndUnit"
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. . S ZR("sp:unit")=$G(@LRN@("units@value"))
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. . S ZR("sp:value")=$G(@LRN@("high@value"))
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. . D ADDINN^C0XF2N(C0SGRF,MAXNM,.ZR)
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. . K ZR
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. . ;
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. . ; create the minimum graph
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. . ;
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. . S ZR("rdf:type")="sp:ValueAndUnit"
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. . S ZR("sp:unit")=$G(@LRN@("units@value"))
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. . S ZR("sp:value")=$G(@LRN@("low@value"))
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. . D ADDINN^C0XF2N(C0SGRF,MINNM,.ZR)
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. . K ZR
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. ;
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. ; create the value and unit graph
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. ;
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. S ZR("rdf:type")="sp:ValueAndUnit"
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. S ZR("sp:unit")=$G(@LRN@("units@value"))
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. I ZR("sp:unit")="" S ZR("sp:unit")="{unknown}" ; was $G(@LRN@("test@value")) gpl
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. S ZR("sp:value")=$G(@LRN@("result@value"))
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. D ADDINN^C0XF2N(C0SGRF,VUNM,.ZR)
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. K ZR
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. ;
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. ; create specimen collected graph
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. ;
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. S ZR("rdf:type")="sp:Attribution"
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. S ZR("sp:startDate")=$$SPDATE^C0SUTIL($G(@LRN@("collected@value")))
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. D ADDINN^C0XF2N(C0SGRF,SPECCOLL,.ZR)
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. K ZR
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. ;
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. ; create lab name graph - this contains the test name and code
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. ;
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. I LOINC'="" D ;
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. . S ZR("rdf:type")="sp:CodedValue"
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. . S ZR("dcterms:title")=LABTST
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. . N LOINCNM S LOINCNM="loinc:"_LOINC
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. . S ZR("sp:code")="loinc:"_LOINC
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. . D ADDINN^C0XF2N(C0SGRF,LABNAME,.ZR)
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. . K ZR
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. . S ZR("dcterms:identifier")=LOINC
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. . S ZR("dcterms:title")=LABTST
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. . S ZR("rdf:type")="sp:Code"
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. . S ZR("sp:system")="http://loinc.org/codes/"
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. . D ADDINN^C0XF2N(C0SGRF,LOINCNM,.ZR)
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. . K ZR
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. ;
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. ; that's all for now folks (there is more to do like reference ranges
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. ; and result values)
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. ;
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D BULKLOAD^C0XF2N(.C0XFDA)
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S GRTN=C0SGRF
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Q
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;
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SAMPLE ; import sample lab tests to the triplestore
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N GN
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S GN=$NA(^rdf("lab_results"))
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D INSRDF^C0XF2N(GN,"/smart/lab/samples")
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Q
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;
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