322 lines
16 KiB
Mathematica
322 lines
16 KiB
Mathematica
C0SPROB ; GPL - Smart Problem Processing ;5/01/12 17:05
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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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;
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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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;
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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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;
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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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;
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Q
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;
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; sample VistA NHIN problem list
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;
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;^TMP("C0STBL",91,"problem",1,"acuity@value")="C"
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;^TMP("C0STBL",91,"problem",1,"entered@value")=3110531
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;^TMP("C0STBL",91,"problem",1,"facility@code")=100
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;^TMP("C0STBL",91,"problem",1,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",1,"icd@value")=414.9
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;^TMP("C0STBL",91,"problem",1,"id@value")=100
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;^TMP("C0STBL",91,"problem",1,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",1,"name@value")="Coronary Artery Disease"
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;^TMP("C0STBL",91,"problem",1,"onset@value")=3100201
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;^TMP("C0STBL",91,"problem",1,"provider@code")=63
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;^TMP("C0STBL",91,"problem",1,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",1,"removed@value")=0
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;^TMP("C0STBL",91,"problem",1,"sc@value")=0
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;^TMP("C0STBL",91,"problem",1,"status@value")="A"
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;^TMP("C0STBL",91,"problem",1,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",1,"updated@value")=3110531
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;^TMP("C0STBL",91,"problem",2,"acuity@value")="C"
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;^TMP("C0STBL",91,"problem",2,"entered@value")=3110602
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;^TMP("C0STBL",91,"problem",2,"facility@code")=100
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;^TMP("C0STBL",91,"problem",2,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",2,"icd@value")=780.2
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;^TMP("C0STBL",91,"problem",2,"id@value")=108
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;^TMP("C0STBL",91,"problem",2,"name@value")="Syncope and collapse"
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;^TMP("C0STBL",91,"problem",2,"onset@value")=3110102
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;^TMP("C0STBL",91,"problem",2,"provider@code")=63
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;^TMP("C0STBL",91,"problem",2,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",2,"removed@value")=0
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;^TMP("C0STBL",91,"problem",2,"sc@value")=0
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;^TMP("C0STBL",91,"problem",2,"status@value")="A"
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;^TMP("C0STBL",91,"problem",2,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",2,"updated@value")=3110602
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;^TMP("C0STBL",91,"problem",3,"acuity@value")="C"
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;^TMP("C0STBL",91,"problem",3,"entered@value")=3110602
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;^TMP("C0STBL",91,"problem",3,"facility@code")=100
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;^TMP("C0STBL",91,"problem",3,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",3,"icd@value")=433.91
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;^TMP("C0STBL",91,"problem",3,"id@value")=109
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;^TMP("C0STBL",91,"problem",3,"name@value")="Occlusion and Stenosis of Unspecifid Precerebral Artery with Cerebral Infarctio"
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;^TMP("C0STBL",91,"problem",3,"onset@value")=3100101
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;^TMP("C0STBL",91,"problem",3,"provider@code")=63
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;^TMP("C0STBL",91,"problem",3,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",3,"removed@value")=0
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;^TMP("C0STBL",91,"problem",3,"sc@value")=0
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;^TMP("C0STBL",91,"problem",3,"status@value")="A"
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;^TMP("C0STBL",91,"problem",3,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",3,"updated@value")=3110602
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;^TMP("C0STBL",91,"problem",4,"entered@value")=3110603
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;^TMP("C0STBL",91,"problem",4,"facility@code")=100
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;^TMP("C0STBL",91,"problem",4,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",4,"icd@value")="00.66"
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;^TMP("C0STBL",91,"problem",4,"id@value")=115
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;^TMP("C0STBL",91,"problem",4,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",4,"name@value")="00.66"
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;^TMP("C0STBL",91,"problem",4,"provider@code")=63
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;^TMP("C0STBL",91,"problem",4,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",4,"removed@value")=0
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;^TMP("C0STBL",91,"problem",4,"status@value")="A"
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;^TMP("C0STBL",91,"problem",4,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",4,"updated@value")=3110603
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;^TMP("C0STBL",91,"problem",5,"entered@value")=3110603
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;^TMP("C0STBL",91,"problem",5,"facility@code")=100
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;^TMP("C0STBL",91,"problem",5,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",5,"icd@value")=37.21
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;^TMP("C0STBL",91,"problem",5,"id@value")=116
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;^TMP("C0STBL",91,"problem",5,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",5,"name@value")=37.21
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;^TMP("C0STBL",91,"problem",5,"provider@code")=63
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;^TMP("C0STBL",91,"problem",5,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",5,"removed@value")=0
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;^TMP("C0STBL",91,"problem",5,"status@value")="A"
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;^TMP("C0STBL",91,"problem",5,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",5,"updated@value")=3110603
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;^TMP("C0STBL",91,"problem",6,"entered@value")=3110603
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;^TMP("C0STBL",91,"problem",6,"facility@code")=100
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;^TMP("C0STBL",91,"problem",6,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",6,"icd@value")=81.51
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;^TMP("C0STBL",91,"problem",6,"id@value")=117
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;^TMP("C0STBL",91,"problem",6,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",6,"name@value")=81.51
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;^TMP("C0STBL",91,"problem",6,"provider@code")=63
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;^TMP("C0STBL",91,"problem",6,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",6,"removed@value")=0
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;^TMP("C0STBL",91,"problem",6,"status@value")="A"
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;^TMP("C0STBL",91,"problem",6,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",6,"updated@value")=3110603
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;^TMP("C0STBL",91,"problem",7,"entered@value")=3110603
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;^TMP("C0STBL",91,"problem",7,"facility@code")=100
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;^TMP("C0STBL",91,"problem",7,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",7,"icd@value")=47.09
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;^TMP("C0STBL",91,"problem",7,"id@value")=118
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;^TMP("C0STBL",91,"problem",7,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",7,"name@value")=47.09
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;^TMP("C0STBL",91,"problem",7,"provider@code")=63
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;^TMP("C0STBL",91,"problem",7,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",7,"removed@value")=0
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;^TMP("C0STBL",91,"problem",7,"status@value")="A"
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;^TMP("C0STBL",91,"problem",7,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",7,"updated@value")=3110603
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;^TMP("C0STBL",91,"problem",8,"entered@value")=3110603
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;^TMP("C0STBL",91,"problem",8,"facility@code")=100
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;^TMP("C0STBL",91,"problem",8,"facility@name")="VOE OFFICE INSTITUTION"
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;^TMP("C0STBL",91,"problem",8,"icd@value")="250.00"
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;^TMP("C0STBL",91,"problem",8,"id@value")=119
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;^TMP("C0STBL",91,"problem",8,"location@value")="DR OFFICE"
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;^TMP("C0STBL",91,"problem",8,"name@value")="Diabetes Mellitus without mentionof Complication, type II or unspecified type,"
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;^TMP("C0STBL",91,"problem",8,"provider@code")=63
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;^TMP("C0STBL",91,"problem",8,"provider@name")="KING,MATTHEW MICHAEL"
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;^TMP("C0STBL",91,"problem",8,"removed@value")=0
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;^TMP("C0STBL",91,"problem",8,"status@value")="A"
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;^TMP("C0STBL",91,"problem",8,"unverified@value")=0
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;^TMP("C0STBL",91,"problem",8,"updated@value")=3110603
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;
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; sample Smart lab result triples
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;
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;G("node16rk1fgdvx10882","code")="snomed:40930008"
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;G("node16rk1fgdvx10882","dcterms:title")="Hypothyroidism"
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;G("node16rk1fgdvx10882","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11051","code")="snomed:188155002"
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;G("node16rk1fgdvx11051","dcterms:title")="Primary malignant neoplasm of lower outer quadrant of female breast"
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;G("node16rk1fgdvx11051","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11073","code")="snomed:353295004"
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;G("node16rk1fgdvx11073","dcterms:title")="Toxic diffuse goiter"
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;G("node16rk1fgdvx11073","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11089","code")="snomed:54302000"
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;G("node16rk1fgdvx11089","dcterms:title")="Disorder of breast"
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;G("node16rk1fgdvx11089","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11351","code")="snomed:38341003"
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;G("node16rk1fgdvx11351","dcterms:title")="Essential hypertension"
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;G("node16rk1fgdvx11351","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11390","code")="snomed:44054006"
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;G("node16rk1fgdvx11390","dcterms:title")="Diabetes mellitus type 2"
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;G("node16rk1fgdvx11390","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11558","code")="snomed:195967001"
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;G("node16rk1fgdvx11558","dcterms:title")="Asthma"
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;G("node16rk1fgdvx11558","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11578","code")="snomed:254837009"
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;G("node16rk1fgdvx11578","dcterms:title")="Primary malignant neoplasm of female breast"
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;G("node16rk1fgdvx11578","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11687","code")="snomed:8517006"
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;G("node16rk1fgdvx11687","dcterms:title")="History of tobacco use"
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;G("node16rk1fgdvx11687","rdf:type")="sp:CodedValue"
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;G("node16rk1fgdvx11716","code")="snomed:55822004"
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;G("node16rk1fgdvx11716","dcterms:title")="Hyperlipidemia"
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;G("node16rk1fgdvx11716","rdf:type")="sp:CodedValue"
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;G("smart:1577780/problems/69560e4721e1","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/69560e4721e1","problemName")="node16rk1fgdvx11089"
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;G("smart:1577780/problems/69560e4721e1","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/69560e4721e1","startDate")="2005-08-02"
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;G("smart:1577780/problems/06ef10c4e92c","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/06ef10c4e92c","problemName")="node16rk1fgdvx11051"
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;G("smart:1577780/problems/06ef10c4e92c","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/06ef10c4e92c","startDate")="2006-02-20"
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;G("smart:1577780/problems/9894ba9dfe5a","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/9894ba9dfe5a","problemName")="node16rk1fgdvx11578"
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;G("smart:1577780/problems/9894ba9dfe5a","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/9894ba9dfe5a","startDate")="2005-08-22"
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;G("smart:1577780/problems/c109aa7a0675","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/c109aa7a0675","problemName")="node16rk1fgdvx11558"
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;G("smart:1577780/problems/c109aa7a0675","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/c109aa7a0675","startDate")="2005-09-22"
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;G("smart:1577780/problems/1c50100614a2","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/1c50100614a2","problemName")="node16rk1fgdvx11073"
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;G("smart:1577780/problems/1c50100614a2","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/1c50100614a2","startDate")="2007-02-21"
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;G("smart:1577780/problems/083dffb2c4a0","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/083dffb2c4a0","problemName")="node16rk1fgdvx11390"
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;G("smart:1577780/problems/083dffb2c4a0","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/083dffb2c4a0","startDate")="2007-01-07"
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;G("smart:1577780/problems/762b5639a2d1","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/762b5639a2d1","problemName")="node16rk1fgdvx11687"
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;G("smart:1577780/problems/762b5639a2d1","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/762b5639a2d1","startDate")="2006-02-20"
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;G("smart:1577780/problems/9dc9053dd6f4","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/9dc9053dd6f4","problemName")="node16rk1fgdvx11716"
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;G("smart:1577780/problems/9dc9053dd6f4","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/9dc9053dd6f4","startDate")="2008-04-08"
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;G("smart:1577780/problems/e3fe9b7ee552","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/e3fe9b7ee552","problemName")="node16rk1fgdvx10882"
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;G("smart:1577780/problems/e3fe9b7ee552","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/e3fe9b7ee552","startDate")="2005-10-27"
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;G("smart:1577780/problems/9933307e8f95","belongsTo")="smart:1577780"
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;G("smart:1577780/problems/9933307e8f95","problemName")="node16rk1fgdvx11351"
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;G("smart:1577780/problems/9933307e8f95","rdf:type")="sp:Problem"
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;G("smart:1577780/problems/9933307e8f95","startDate")="2005-08-22"
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;G("snomed:188155002","dcterms:identifier")=188155002
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;G("snomed:188155002","dcterms:title")="Primary malignant neoplasm of lower outer quadrant of female breast"
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;G("snomed:188155002","rdf:type")="sp:Code"
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;G("snomed:188155002","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:195967001","dcterms:identifier")=195967001
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;G("snomed:195967001","dcterms:title")="Asthma"
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;G("snomed:195967001","rdf:type")="sp:Code"
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;G("snomed:195967001","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:254837009","dcterms:identifier")=254837009
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;G("snomed:254837009","dcterms:title")="Primary malignant neoplasm of female breast"
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;G("snomed:254837009","rdf:type")="sp:Code"
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;G("snomed:254837009","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:353295004","dcterms:identifier")=353295004
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;G("snomed:353295004","dcterms:title")="Toxic diffuse goiter"
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;G("snomed:353295004","rdf:type")="sp:Code"
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;G("snomed:353295004","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:38341003","dcterms:identifier")=38341003
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;G("snomed:38341003","dcterms:title")="Essential hypertension"
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;G("snomed:38341003","rdf:type")="sp:Code"
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;G("snomed:38341003","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:40930008","dcterms:identifier")=40930008
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;G("snomed:40930008","dcterms:title")="Hypothyroidism"
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;G("snomed:40930008","rdf:type")="sp:Code"
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;G("snomed:40930008","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:44054006","dcterms:identifier")=44054006
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;G("snomed:44054006","dcterms:title")="Diabetes mellitus type 2"
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;G("snomed:44054006","rdf:type")="sp:Code"
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;G("snomed:44054006","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:54302000","dcterms:identifier")=54302000
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;G("snomed:54302000","dcterms:title")="Disorder of breast"
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;G("snomed:54302000","rdf:type")="sp:Code"
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;G("snomed:54302000","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:55822004","dcterms:identifier")=55822004
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;G("snomed:55822004","dcterms:title")="Hyperlipidemia"
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;G("snomed:55822004","rdf:type")="sp:Code"
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;G("snomed:55822004","system")="http://purl.bioontology.org/ontology/SNOMEDCT"
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;G("snomed:8517006","dcterms:identifier")=8517006
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;G("snomed:8517006","dcterms:title")="History of tobacco use"
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;G("snomed:8517006","rdf:type")="sp:Code"
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;G("snomed:8517006","system")="http://purl.bioontology.org/ontology/SNOMEDCT/"
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;
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PROB(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 problems
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;
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I $O(C0SARY("problem",""))="" D Q ;
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. I $D(DEBUG) W !,"No Problems"
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S GRTN="" ; default to no problems
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N C0SGRF
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S C0SGRF="vistaSmart:"_ZPATID_"/problems"
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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("problem",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("problem",ZI)) ; base for values in this lab result
|
|
. ;
|
|
. N PROBID ; unique Id for this problem
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. S PROBID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
|
|
. ;
|
|
. ; i don't like this because the same problems gets a
|
|
. ; different ID every time it's reported. Can't trace it back to VistA
|
|
. ; I'd rather be using id@value ie "id@value")="118"
|
|
. ;
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|
. N SNOMED S SNOMED=$G(@LRN@("icd@value"))
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. N SNOGRF S SNOGRF="snomed:"_SNOMED
|
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. N SNOTIT S SNOTIT=$G(@LRN@("name@value"))
|
|
. I $D(DEBUG) D ;
|
|
. . W !,"Processing Problem List ",PROBID
|
|
. . W !,"problem: ",SNOTIT
|
|
. . W !,"code: ",SNOMED
|
|
. ;
|
|
. ; first do the base result graph
|
|
. ;
|
|
. S ZR("rdf:type")="sp:Problem"
|
|
. S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's problems
|
|
. ; ie /vista/smart/99912345/problems
|
|
. ;
|
|
. N PROBNAME S PROBNAME=$$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
|
|
;
|