118 lines
4.1 KiB
Mathematica
118 lines
4.1 KiB
Mathematica
C0SPROB ; GPL - Smart Problem Processing ;5/01/12 17:05
|
|
;;0.1;C0S;nopatch;noreleasedate;Build 2
|
|
;Copyright 2012 George Lilly. Licensed under the terms of the GNU
|
|
;General Public License See attached copy of the License.
|
|
;
|
|
;This program is free software; you can redistribute it and/or modify
|
|
;it under the terms of the GNU General Public License as published by
|
|
;the Free Software Foundation; either version 2 of the License, or
|
|
;(at your option) any later version.
|
|
;
|
|
;This program is distributed in the hope that it will be useful,
|
|
;but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;GNU General Public License for more details.
|
|
;
|
|
;You should have received a copy of the GNU General Public License along
|
|
;with this program; if not, write to the Free Software Foundation, Inc.,
|
|
;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
|
;
|
|
Q
|
|
;
|
|
; sample VistA NHIN problem list
|
|
;
|
|
G("node16rk1fgdvx276397","code")="loinc:8480-6"
|
|
G("node16rk1fgdvx276397","dcterms:title")="systolic blood pressure"
|
|
G("node16rk1fgdvx276397","rdf:type")="sp:CodedValue"
|
|
G("node16rk1fgdvx276398","rdf:type")="sp:VitalSign"
|
|
G("node16rk1fgdvx276398","unit")="mm[Hg]"
|
|
G("node16rk1fgdvx276398","value")="113.0"
|
|
G("node16rk1fgdvx276398","vitalName")="node16rk1fgdvx276397"
|
|
|
|
;
|
|
VITALS(GRTN,C0SARY) ; GRTN, passed by reference,
|
|
; is the return name of the graph created. "" if none
|
|
; C0SARY is passed in by reference and is the NHIN array of problems
|
|
;
|
|
I $O(C0SARY("vital",""))="" D Q ;
|
|
. I $D(DEBUG) W !,"No Vital Signs"
|
|
S GRTN="" ; default to no vital signs
|
|
N C0SGRF
|
|
S C0SGRF="/vista/smart/"_ZPATID_"/vitals"
|
|
I $D(DEBUG) W !,"Processing ",C0SGRF
|
|
D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph
|
|
D INITFARY^C0XF2N("C0XFARY") ; which triple store to use
|
|
N FARY S FARY="C0XFARY"
|
|
D USEFARY^C0XF2N(FARY)
|
|
D VOCINIT^C0XUTIL
|
|
;
|
|
D STARTADD^C0XF2N ; initialize to create triples
|
|
;
|
|
N ZI S ZI=""
|
|
F S ZI=$O(C0SARY("vital",ZI)) Q:ZI="" D ;
|
|
. N LRN,ZR ; ZR is the local array for building the new triples
|
|
. S LRN=$NA(C0SARY("problem",ZI)) ; base for values in this lab result
|
|
. ;
|
|
. N PROBID ; unique Id for this problem
|
|
. S PROBID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
|
|
. ;
|
|
. ; i don't like this because the same problems gets a
|
|
. ; different ID every time it's reported. Can't trace it back to VistA
|
|
. ; I'd rather be using id@value ie "id@value")="118"
|
|
. ;
|
|
. N SNOMED,ICD S ICD=$G(@LRN@("icd@value"))
|
|
. S SNOMED=$$SNOMED(ICD) ; look up the snomed code in the map
|
|
. I SNOMED="" S SNOMED=ICD ; if not found, return the ICD code
|
|
. N SNOGRF S SNOGRF="snomed:"_SNOMED
|
|
. N SNOTIT S SNOTIT=$G(@LRN@("name@value"))
|
|
. I $D(DEBUG) D ;
|
|
. . W !,"Processing Problem List ",PROBID
|
|
. . W !,"problem: ",SNOTIT
|
|
. . W !,"code: ",SNOMED
|
|
. ;
|
|
. ; first do the base result graph
|
|
. ;
|
|
. S ZR("rdf:type")="sp:Problem"
|
|
. S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's problems
|
|
. ; ie /vista/smart/99912345/problems
|
|
. ;
|
|
. N PROBNAME S PROBNAME=$$ANONS^C0XF2N ; new node for problem name
|
|
. S ZR("sp:problemName")=PROBNAME
|
|
. ;
|
|
. N STARTDT S STARTDT=$$SPDATE^C0SUTIL($G(@LRN@("entered@value")))
|
|
. S ZR("sp:startDate")=STARTDT
|
|
. ;
|
|
. D ADDINN^C0XF2N(C0SGRF,PROBID,.ZR) ; addIfNotNull the triples
|
|
. K ZR ; clean up
|
|
. ;
|
|
. ; create the problemName graph
|
|
. ;
|
|
. S ZR("rdf:type")="sp:CodedValue"
|
|
. S ZR("sp:code")="snomed:"_SNOMED
|
|
. S ZR("dcterms:title")=$G(@LRN@("name@value"))
|
|
. D ADDINN^C0XF2N(C0SGRF,PROBNAME,.ZR)
|
|
. K ZR
|
|
. ;
|
|
. ; create snomed graph
|
|
. ;
|
|
. S ZR("rdf:type")="sp:Code"
|
|
. S ZR("sp:system")="http://purl.bioontology.org/ontology/SNOMEDCT"
|
|
. S ZR("dcterms:identifier")=SNOMED
|
|
. S ZR("dcterms:title")=SNOTIT
|
|
. D ADDINN^C0XF2N(C0SGRF,SNOGRF,.ZR)
|
|
. K ZR
|
|
. ;
|
|
D BULKLOAD^C0XF2N(.C0XFDA)
|
|
S GRTN=C0SGRF
|
|
Q
|
|
;
|
|
SNOMED(ZICD) ; extrinsic which returns SNOMED code given an ICD9 code
|
|
; requires the mapping table installed in the triplestore
|
|
;
|
|
N ZSN,ZARY,ZSUB
|
|
S ZSUB=$$subject^C0XGET1(,ZICD) ; subject of the ICD9 code
|
|
D objects^C0XGET1(.ZARY,ZSUB,"cg:ontology#toCode")
|
|
S ZSN=$O(ZARY(""))
|
|
I $D(DEBUG) W !,ZSN," ",$$object^C0XGET1(ZSUB,"rdfs:label")
|
|
Q ZSN
|
|
; |