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From chen...@apache.org
Subject svn commit: r1620453 - in /ctakes/trunk/ctakes-ytex/scripts/data: hsql/umls/ mssql/esld/ mssql/umls/ mysql/umls/ orcl/umls/
Date Mon, 25 Aug 2014 21:21:25 GMT
Author: chenpei
Date: Mon Aug 25 21:21:24 2014
New Revision: 1620453

URL: http://svn.apache.org/r1620453
Log:
CTAKES-309 Add 'SNOMEDCT_US' to ytext db scripts in addition to 'SNOMEDCT'.  This is to support
those who use later versions of UMLS.

Modified:
    ctakes/trunk/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/create_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/insert_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/readme.txt
    ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/readme.txt
    ctakes/trunk/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql

Modified: ctakes/trunk/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql Mon Aug 25 21:21:24 2014
@@ -20,7 +20,7 @@
 insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, stem_str)
 select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str
 from umls_aui_fword c
-inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'RXNORM')
+inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'SNOMEDCT_US', 'RXNORM')
 inner join 
 (
 	select cui, min(tui) tui

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/create_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/create_view.sql?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/create_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/create_view.sql Mon Aug 25 21:21:24 2014
@@ -73,7 +73,7 @@ where 
 	'T019','T020','T037','T046','T047','T048','T049','T050','T190','T191',
 	'T033','T034','T040','T041','T042','T043','T044','T045','T046','T056','T057','T184'
 	)
-	and sourcetype = 'SNOMEDCT'
+	and sourcetype in ('SNOMEDCT', 'SNOMEDCT_US')
 ) 
 or cui in (
 	'C0079304', /* EGD */

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/insert_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/insert_view.sql?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/insert_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/insert_view.sql Mon Aug 25 21:21:24 2014
@@ -22,7 +22,7 @@ select mrc.cui, t.tui, c.fword, c.fstem,
 from $(db_schema).umls_aui_fword c
 inner join $(umls_catalog).$(umls_schema).MRCONSO mrc 
 	on c.aui = mrc.aui
-	and mrc.sab in ( 'SNOMEDCT','RXNORM' )
+	and mrc.sab in ( 'SNOMEDCT', 'SNOMEDCT_US', 'RXNORM' )
 inner join 
 (
 	select cui, min(tui) tui

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/readme.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/readme.txt?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/readme.txt (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/umls/readme.txt Mon Aug 25 21:21:24 2014
@@ -2,12 +2,12 @@
 rmdir /s /q E:\projects\ytex-umls\mssql
 mkdir E:\projects\ytex-umls\mssql
 cd /d E:\projects\ytex-umls\mssql
-bcp "select * from umls..MRCONSO where SAB in ('SNOMEDCT', 'RXNORM', 'SRC') and LAT = 'ENG'"
queryout MRCONSO.bcp -S localhost -T -n
-bcp "select * from umls..MRSTY where CUI in (select distinct CUI from umls..MRCONSO where
SAB in ('SNOMEDCT', 'RXNORM', 'SRC'))" queryout MRSTY.bcp -S localhost -T -n
-bcp "select * from YTEX_TEST.dbo.umls_aui_fword where aui in (select distinct AUI from umls..MRCONSO
where SAB in ('SNOMEDCT', 'RXNORM', 'SRC'))" queryout umls_aui_fword.bcp -S localhost -T -n
+bcp "select * from umls..MRCONSO where SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC')
and LAT = 'ENG'" queryout MRCONSO.bcp -S localhost -T -n
+bcp "select * from umls..MRSTY where CUI in (select distinct CUI from umls..MRCONSO where
SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC'))" queryout MRSTY.bcp -S localhost -T -n
+bcp "select * from YTEX_TEST.dbo.umls_aui_fword where aui in (select distinct AUI from umls..MRCONSO
where SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC'))" queryout umls_aui_fword.bcp -S
localhost -T -n
 
 @rem export examples using this:
 cd E:\projects\ytex\data\mssql\umls
-bcp "select * from umls..MRCONSO where CUI in (select distinct code from YTEX_TEST.dbo.anno_ontology_concept)
and SAB in ('SNOMEDCT', 'RXNORM', 'SRC') and LAT = 'ENG'" queryout MRCONSO.bcp -S localhost
-T -n
+bcp "select * from umls..MRCONSO where CUI in (select distinct code from YTEX_TEST.dbo.anno_ontology_concept)
and SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC') and LAT = 'ENG'" queryout MRCONSO.bcp
-S localhost -T -n
 bcp "select * from umls..MRSTY where CUI in (select distinct code from YTEX_TEST.dbo.anno_ontology_concept)"
queryout MRSTY.bcp -S localhost -T -n
-bcp "select * from YTEX_TEST.dbo.umls_aui_fword where aui in (select AUI from umls..MRCONSO
m inner join (select distinct code from YTEX_TEST.dbo.anno_ontology_concept) c on m.cui =
c.code where SAB='SNOMEDCT')" queryout umls_aui_fword.bcp -S localhost -T -n
+bcp "select * from YTEX_TEST.dbo.umls_aui_fword where aui in (select AUI from umls..MRCONSO
m inner join (select distinct code from YTEX_TEST.dbo.anno_ontology_concept) c on m.cui =
c.code where SAB in ('SNOMEDCT', 'SNOMEDCT_US'))" queryout umls_aui_fword.bcp -S localhost
-T -n

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql Mon Aug 25 21:21:24
2014
@@ -24,7 +24,7 @@
 insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, stem_str)
 select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str
 from umls_aui_fword c
-inner join @UMLS_SCHEMA@.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'RXNORM')
+inner join @UMLS_SCHEMA@.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'SNOMEDCT_US',
'RXNORM')
 inner join 
 (
 	select cui, min(tui) tui

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/readme.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/readme.txt?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/readme.txt (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/readme.txt Mon Aug 25 21:21:24 2014
@@ -49,14 +49,14 @@ inner join
 (
 select distinct code from anno_ontology_concept
 ) c on mrc.cui = c.code
-where mrc.sab in ( 'SNOMEDCT', 'RXNORM', 'SRC')
+where mrc.sab in ( 'SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC')
 and lat = 'ENG'
 ;
 
 select fw.*
 into outfile 'E:/projects/ytex/data/mysql/umls/umls_aui_fword.txt'
 from umls_aui_fword fw
-inner join umls.mrconso mrc on fw.aui = mrc.aui and mrc.sab in ( 'SNOMEDCT', 'RXNORM', 'SRC')
+inner join umls.mrconso mrc on fw.aui = mrc.aui and mrc.sab in ( 'SNOMEDCT', 'SNOMEDCT_US',
'RXNORM', 'SRC')
 inner join
 (
 select distinct code from anno_ontology_concept
@@ -85,7 +85,7 @@ coalesce(CVF,'')
 into outfile 'E:/projects/ytex-umls/mysql/MRCONSO.RRF'
 fields terminated by '|' ESCAPED BY '' lines terminated by '\r\n'
 from umls.MRCONSO mrc
-where SAB in ('SNOMEDCT', 'RXNORM', 'SRC')
+where SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC')
 and LAT = 'ENG'
 ;
 
@@ -104,13 +104,13 @@ inner join
 	(
 	select distinct cui
 	from umls.MRCONSO
-	where SAB in ('SNOMEDCT', 'RXNORM', 'SRC')
+	where SAB in ('SNOMEDCT', 'SNOMEDCT_US', 'RXNORM', 'SRC')
 	) c on sty.cui = c.cui
 ;
 
 select fw.*
 into outfile 'E:/projects/ytex-umls/mysql/umls_aui_fword.txt'
 from umls_aui_fword fw
-inner join umls.mrconso mrc on fw.aui = mrc.aui and mrc.sab in ('SNOMEDCT', 'RXNORM', 'SRC')
+inner join umls.mrconso mrc on fw.aui = mrc.aui and mrc.sab in ('SNOMEDCT', 'SNOMEDCT_US',
'RXNORM', 'SRC')
 ;
 

Modified: ctakes/trunk/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql?rev=1620453&r1=1620452&r2=1620453&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql Mon Aug 25 21:21:24
2014
@@ -20,7 +20,7 @@
 insert into v_snomed_fword_lookup
 select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str
 from umls_aui_fword c
-inner join @UMLS_SCHEMA@.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'RXNORM')
+inner join @UMLS_SCHEMA@.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'SNOMEDCT_US',
'RXNORM')
 inner join 
 (
 	select cui, min(tui) tui



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