Update to UMLS 2014AB. Main change is removal of MRCOC.

Make COC support based on umlisp::mrcoc in *features*

diff --git a/class-support.lisp b/class-support.lisp
index 0352c742f0b5523876603b003ae1c92b4b4a96e9..47463dd194610fb454fc6a7b5a37ff484bf58cb5 100644 (file)
--- a/class-support.lisp
+++ b/class-support.lisp
@@ -291,6 +291,7 @@
         (sort (copy-seq f) 'string-lessp :key 'u::pfstr2)
         f)))
 
+#+mrcoc
 (defun filter-ucocs (ucocs &key (remove-duplicate-pfstr2 t) (sort :pfstr2))
   (when remove-duplicate-pfstr2
     (setq ucocs (remove-duplicates ucocs :test 'equal :key 'u::pfstr2)))
@@ -364,6 +365,8 @@
 
 
 #+scl
-(dolist (c '(urank udef usat uso ucxt ustr uterm usty urel ucoc uatx uconso uxw uxnw uxns lexterm labr lagr lcmp lmod lnom lprn lprp lspl ltrm ltyp lwd sdef sstr sstre1 sstre2 usrl))
+(dolist (c '(urank udef usat uso ucxt ustr uterm usty urel
+             #+mrcoc ucoc
+             uatx uconso uxw uxnw uxns lexterm labr lagr lcmp lmod lnom lprn lprp lspl ltrm ltyp lwd sdef sstr sstre1 sstre2 usrl))
     (let ((cl (find-class c)))
       (clos:finalize-inheritance cl)))

diff --git a/classes.lisp b/classes.lisp
index 05af0fbf36fe4fc0ceb49dcbbe01796453cd1c1c..1c656299575a35e334ae89ac3b442bd96de44f8f 100644 (file)
--- a/classes.lisp
+++ b/classes.lisp
@@ -194,6 +194,7 @@
   (:user-name "Relationship")
   (:default-print-slots stype1 rel cui2 aui2 stype2 rela rui srui sab sl rg dir suppress pfstr2))
 
+#+mrcoc
 (defclass ucoc (umlsclass)
   ((cui1 :value-type fixnum :initarg :cui1 :reader cui1 :print-formatter fmt-cui)
    (aui1 :value-type fixnum :initarg :aui1 :reader aui1 :print-formatter fmt-aui)
@@ -227,7 +228,8 @@
    (s#term :reader s#term :subobject (find-uterm-cui cui))
    (s#sat :reader s#sat :subobject (find-usat-ui cui))
    (s#rel :reader s#rel :subobject (find-urel-cui cui))
-   (s#coc :reader s#coc :subobject (find-ucoc-cui cui)))
+   #+mrcoc (s#coc :reader s#coc :subobject (find-ucoc-cui cui))
+   )
   (:metaclass hyperobject-class)
   (:user-name "Concept")
   (:default-print-slots cui lrl pfstr))
@@ -270,7 +272,8 @@
    (s#term :reader s#term :subobject (find-uterm-cui cui))
    (s#sat :reader s#sat :subobject (find-usat-ui cui))
    (s#rel :reader s#rel :subobject (find-urel-cui cui))
-   (s#coc :reader s#coc :subobject (find-ucoc-cui cui)))
+   #+mrcoc (s#coc :reader s#coc :subobject (find-ucoc-cui cui))
+   )
   (:documentation "CONSO is a new concept from the RRF files.")
   (:metaclass hyperobject-class)
   (:user-name "Concept")

diff --git a/composite.lisp b/composite.lisp
index afd3e16176a3a81f437f622a28cc7924834edfd2..1c453e1805c31b9cf8823a9f642703cdf6c6842f 100644 (file)
--- a/composite.lisp
+++ b/composite.lisp
@@ -50,7 +50,7 @@
     (funcall related-con-func ucon))
    :key #'cui))
 
-(defun find-ucon2-coc-tui (ucon tui)
+#+mrcoc (defun find-ucon2-coc-tui (ucon tui)
   "Return list of ucon's that have co-occuring concepts of semantic type tui"
   (find-ucon2-tui ucon tui #'cui2 #'s#coc))
 
@@ -124,7 +124,7 @@
               freqs)))
     (sort freqs #'> :key #'freq)))
 
-(defun find-ucon2_freq-coc-tui (ucon tui)
+#+mrcoc (defun find-ucon2_freq-coc-tui (ucon tui)
 "Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui"
   (let ((ucon_freqs '()))
     (dolist (ucoc (s#coc ucon))
@@ -145,7 +145,7 @@
         (funcall lookup-func ucon (tui usty))
       nil)))
 
-(defun find-ucon2-coc-str&sty (str sty)
+#+mrcoc (defun find-ucon2-coc-str&sty (str sty)
   "Find all ucons that are a co-occuring concept for concept named str
    and that have semantic type of sty"
   (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))
@@ -178,7 +178,7 @@
   "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
   (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))
 
-(defun find-ucon2_freq-coc-tui-all (tui)
+#+mrcoc (defun find-ucon2_freq-coc-tui-all (tui)
   (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
 
 #+(or scl)

diff --git a/create-sql.lisp b/create-sql.lisp
index 27f65de0b431681ea6c3a5148b6cfea2a922d13c..20964f5c4ae3a6a8f4023ecf033582a759061856 100644 (file)
--- a/create-sql.lisp
+++ b/create-sql.lisp
@@ -292,7 +292,7 @@
     (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
     (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
     (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
-    (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
+#+mrcoc (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
     (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
     (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
     (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)

diff --git a/data-structures.lisp b/data-structures.lisp
index 10e1c0c38f2e07bba00a417398c11ae114e3b9f6..d76a5c23697e18379dc2e36df819554ca20f5f33 100644 (file)
--- a/data-structures.lisp
+++ b/data-structures.lisp
@@ -18,7 +18,7 @@
 
 ;;; Paths for files
 
-(defparameter *release* "2011AA")
+(defparameter *release* "2014AB")
 
 (defparameter *umls-path*
   (make-pathname :directory (list :absolute "srv" "umls" *release* *release*))
@@ -111,5 +111,3 @@
 (defmethod print-object ((obj ucol) s)
   (print-unreadable-object (obj s :type t)
     (format s "~A" (col obj))))
-
-

diff --git a/package.lisp b/package.lisp
index 63d442b7c331ebeab3b0105c329a102dfb305efc..7d925a425a56477b59f5b8e8eedd55b25ba572e1 100644 (file)
--- a/package.lisp
+++ b/package.lisp
@@ -26,7 +26,8 @@
      ;; From classes.lisp
      #1=(#:umlsclass
          #:ucon #:uterm #:ustr #:usrl #:uso #:urank #:udef #:usat #:usab
-         #:urel #:ucoc #:usty #:uxw #:uxnw  #:uxns
+         #:urel
+         #:usty #:uxw #:uxnw  #:uxns
          #:lexterm #:labr #:lagr #:lcmp #:lmod #:lnom #:lprn #:lprp #:lspl #:ltrm
          #:ltyp #:lwd #:sdef #:sstr #:sstre1 #:sstre2
          #:sty #:tui #:def #:sab #:srl #:tty #:rank #:suppress #:atn #:atv #:vcui
@@ -35,7 +36,7 @@
          #:rl #:sty2 #:ui #:ui2 #:ui3 #:eui #:bas #:eui2 #:bas2 #:rui
          #:cui #:aui #:lui #:sui #:wd #:lat #:nstr :cuilist
          #:rsab #:lat
-         #:s#def #:s#sty #:s#term #:s#str #:s#lo #:s#sat #:s#rel #:s#coc
+         #:s#def #:s#sty #:s#term #:s#str #:s#lo #:s#sat #:s#rel
          #:s#so
          #:pfstr #:pfstr2 #:lrl #:def #:ts #:cui1 #:cui2 #:rela #:sl #:mg #:rel
          #:soc #:cot #:cof #:coa #:isn #:fr #:un #:sna #:soui #:hcd #:stt #:str
@@ -92,9 +93,6 @@
          #:find-cui2-urel-cui
          #:find-urel-cui2
          #:find-ucon-rel-cui2
-         #:find-ucoc-cui
-         #:find-ucoc-cui2
-         #:find-ucon-coc-cui2
          #:find-usty-sty
          #:suistr
          #:print-umlsclass
@@ -195,15 +193,11 @@
          #:tui-disease-or-syndrome
          #:ucon-is-tui?
          #:find-ucon2-tui
-         #:find-ucon2-coc-tui
          #:find-ucon2-rel-tui
-         #:find-ucon2_freq-coc-tui
          #:find-ucon2-str&sty
-         #:find-ucon2-coc-str&sty
          #:find-ucon2-rel-str&sty
          #:find-ucon2_freq-tui-all
          #:find-ucon2_freq-rel-tui-all
-         #:find-ucon2_freq-coc-tui-all
          #:ucon_freq
          #:ustr_freq
          #:usty_freq
@@ -212,6 +206,11 @@
          ;; from data-structures.lisp
          #:umls-path
          #:set-umls-path
+
+         ;; Removed features
+         ;; MRCOC
+         ;; #:ucoc #:s#coc #:find-ucoc-cui #:find-ucoc-cui2 #:find-ucon-coc-cui2 #:find-ucon2-coc-tui #:find-ucon2_freq-coc-tui #:find-ucon2-coc-str&sty #:find-ucon2_freq-coc-tui-all
+
          )))
 
   (defpackage umlisp-user
@@ -219,5 +218,3 @@
     (:import-from :umlisp . #1#)
     (:export . #1#)
     (:documentation "User package for UMLisp")))
-
-

diff --git a/parse-rrf.lisp b/parse-rrf.lisp
index 65992bf5a6cd792952b2781dbd0a77dce79ca576..5e28ed5ca8a9f82f6cb9c89233e6e677b4fdf5cd 100644 (file)
--- a/parse-rrf.lisp
+++ b/parse-rrf.lisp
@@ -246,11 +246,11 @@ SNOMED SRL changed from 4 to 9. So we create a new scale ~
        (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
       ("MRSTY.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cui-lrlus (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
-      ("MRCOC.RRF" "KLRL" "TINYINT" 0
+      #+mrcoc ("MRCOC.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string
                     (max (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
                          (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
-      ("MRCOC.RRF" "KLRLUS" "TINYINT" 0
+      #+mrcoc ("MRCOC.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string
                     (max (cui-lrlus (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
                          (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
@@ -316,7 +316,7 @@ SNOMED SRL changed from 4 to 9. So we create a new scale ~
                                                  (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))
 
       #+nil  ("MRREL.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRREL.RRF" "CUI2" x)))))
-      #+nil  ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRCOC.RRF" "CUI2" x)))))
+      #+mrcoc  ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRCOC.RRF" "CUI2" x)))))
 
       ("MRSAT.RRF" "KCUILUI" "BIGINT" 0
        (lambda (x) (write-to-string (make-cuilui
@@ -350,12 +350,13 @@ SNOMED SRL changed from 4 to 9. So we create a new scale ~
     "Custom columns to create.(filename, col, sqltype, value-func).")
 
 (defparameter +index-cols+
-    '(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
-      ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
-      ("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
-      ("SCUI" "MRCONSO")
-      ("CUI" "MRDEF")
-      ("CUI1" "MRREL") ("CUI2" "MRREL") ("SAB" "MRREL")
+  '( #+mrcoc ("CUI1" "MRCOC") #+mrcoc ("KLRL" "MRCOC") #+mrcoc ("KLRLUS" "MRCOC")
+    ("CUI" "MRCONSO") ("LUI" "MRCONSO")
+    ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
+    ("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
+    ("SCUI" "MRCONSO")
+    ("CUI" "MRDEF")
+    ("CUI1" "MRREL") ("CUI2" "MRREL") ("SAB" "MRREL")
       ("RUI" "MRREL") ("AUI1" "MRREL") ("AUI2" "MRREL")
       ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
       ("METAUI" "MRSAT") ("ATN" "MRSAT")
@@ -372,8 +373,8 @@ SNOMED SRL changed from 4 to 9. So we create a new scale ~
       ("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
       ("KSRL" "MRDEF") ("KSRL" "MRRANK")("KSRL" "MRREL") ("KSRL" "MRSAT")
       ("KSRLUS" "MRDEF") ("KSRLUS" "MRRANK")("KSRLUS" "MRREL") ("KSRLUS" "MRSAT")
-      ("KLRL" "MRCOC") ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
-      ("KLRLUS" "MRCOC") ("KLRLUS" "MRSTY") ("KLRLUS" "MRXW_ENG") ("KLRLUS" "MRXNW_ENG")
+      ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
+      ("KLRLUS" "MRSTY") ("KLRLUS" "MRXW_ENG") ("KLRLUS" "MRXNW_ENG")
       ("KLRL" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
       ("KLRLUS" "MRXNS_ENG") ("KLRLUS" "MRXW_NONENG")
       ;; LEX indices
@@ -461,6 +462,3 @@ SNOMED SRL changed from 4 to 9. So we create a new scale ~
 (defun gen-ufiles-custom ()
   (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"
               5 0 0 (fields (find-ufile "MRXW_ENG.RRF"))))
-
-
-

diff --git a/sql-classes.lisp b/sql-classes.lisp
index 7736eb6ccc4107bca8f8321d4fa4141bfa75eee4..d1e19f3fea74dd3a36293dab1793f3b24250fad4 100644 (file)
--- a/sql-classes.lisp
+++ b/sql-classes.lisp
@@ -495,7 +495,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                     (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
         collect (find-ucon-cui cui :srl srl)))
 
-(defun find-ucoc-cui (cui &key (srl *current-srl*))
+#+mrcoc (defun find-ucoc-cui (cui &key (srl *current-srl*))
   "Return a list of ucoc for cui"
   (ensure-cui-integer cui)
   (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
@@ -507,7 +507,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                    :cot cot :cof (ensure-integer cof) :coa coa :sab sab
                    :pfstr2 (find-pfstr-cui cui2))))
 
-(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
+#+mrcoc (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
   "Return a list of ucoc for cui2"
   (ensure-cui-integer cui2)
   (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
@@ -518,7 +518,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                    :sab sab :cot cot :cof (ensure-integer cof) :coa coa
                    :pfstr2 (find-pfstr-cui cui2))))
 
-(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
+#+mrcoc (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
   "List of ucon with co-occurance cui2"
   (ensure-cui-integer cui2)
   (mapcar

diff --git a/sql.lisp b/sql.lisp
index 1630562e6830b59fd8d3d9a150487726f6886493..80e068dab7dbc670421eb1696b16fb4070029ec7 100644 (file)
--- a/sql.lisp
+++ b/sql.lisp
@@ -22,8 +22,9 @@
       (:2006ad . "MTS2006AD")
       (:2009ab . "MTS2009AB")
       (:2010aa . "MTS2010AA")
-      (:2012ab . "MTS2012AB")))
-(defvar +default-umls-db+ "MTS2012AA_ALL")
+      (:2012ab . "MTS2012AB")
+      (:2014ab . "MTS2014AB")))
+(defvar +default-umls-db+ "MTS2014AB_ALL")
 
 (defun lookup-db-name (db)
   (cdr (assoc (ensure-keyword db) +umls-sql-map+)))
@@ -39,21 +40,21 @@
     (keyword
      (setq *umls-sql-db* (lookup-db-name db)))))
 
-(defvar *umls-sql-user* "secret")
+(defvar *umls-sql-user* "umls")
 (defun umls-sql-user ()
   *umls-sql-user*)
 (defun set-umls-sql-user (u)
   (sql-disconnect-pooled)
   (setq *umls-sql-user* u))
 
-(defvar *umls-sql-passwd* "secret")
+(defvar *umls-sql-passwd* "umlspw")
 (defun umls-sql-passwd ()
   *umls-sql-passwd*)
 (defun set-umls-sql-passwd (p)
   (sql-disconnect-pooled)
   (setq *umls-sql-passwd* p))
 
-(defvar *umls-sql-host* "localhost")
+(defvar *umls-sql-host* "tiger.med-info.com")
 (defun umls-sql-host ()
   *umls-sql-host*)
 (defun set-umls-sql-host (h)