(defvar *preparse-hash-init?* nil)
(eval-when (:compile-toplevel :load-toplevel :execute)
+
+(declaim (inline srl-to-srlus))
+(defun srl-to-srlus (srl)
+ "Convert the standard SRL category to one oriented for use in the United States.
+Specifically, SRL 4 in the USA has license restrictions between SRL 1 and 2 when
+used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapping is:
+(0->0, 1->1, 4->2, 2->3, 3->4)."
+ (declare (fixnum srl))
+ (cond
+ ((= srl 4) 2)
+ ((= srl 2) 3)
+ ((= srl 3) 4)
+ (t srl)))
+
(let ((pfstr-hash nil) ;; Preferred concept strings by CUI
(cui-lrl-hash nil) ;; LRL by CUI
(lui-lrl-hash nil) ;; LRL by LUI
(sui-lrl-hash nil) ;; LRL by SUI
(cuisui-lrl-hash nil) ;; LRL by CUISUI
- (sab-srl-hash nil)) ;; SRL by SAB
+ (cui-lrlus-hash nil) ;; LRLUS by CUI
+ (lui-lrlus-hash nil) ;; LRLUS by LUI
+ (sui-lrlus-hash nil) ;; LRLUS by SUI
+ (cuisui-lrlus-hash nil) ;; LRL by CUISUI
+
+ (sab-srl-hash nil)
+ (sab-srlus-hash nil)) ;; SRL by SAB
(defun make-preparse-hash-table ()
(if sui-lrl-hash
(clrhash lui-lrl-hash)
(clrhash sui-lrl-hash)
(clrhash cuisui-lrl-hash)
- (clrhash sab-srl-hash))
+ (clrhash cui-lrlus-hash)
+ (clrhash lui-lrlus-hash)
+ (clrhash sui-lrlus-hash)
+ (clrhash cuisui-lrlus-hash)
+ (clrhash sab-srl-hash)
+ (clrhash sab-srlus-hash))
(setf
pfstr-hash (make-hash-table :size 1500000)
cui-lrl-hash (make-hash-table :size 1500000)
lui-lrl-hash (make-hash-table :size 5000000)
sui-lrl-hash (make-hash-table :size 6000000)
cuisui-lrl-hash (make-hash-table :size 6000000)
- sab-srl-hash (make-hash-table :size 200 :test 'equal))))
+ cui-lrlus-hash (make-hash-table :size 1500000)
+ lui-lrlus-hash (make-hash-table :size 5000000)
+ sui-lrlus-hash (make-hash-table :size 6000000)
+ cuisui-lrlus-hash (make-hash-table :size 6000000)
+ sab-srl-hash (make-hash-table :size 200 :test 'equal)
+ sab-srlus-hash (make-hash-table :size 200 :test 'equal))))
(defun ensure-preparse (&optional (force-read nil))
(when (and *preparse-hash-init?* (not force-read))
(declare (fixnum counter)
(ignorable counter))
(with-umls-file (line "MRCONSO.RRF")
- (let ((cui (parse-ui (nth 0 line)))
- (lui (parse-ui (nth 3 line)))
- (sui (parse-ui (nth 5 line)))
- (sab (nth 11 line))
- (srl (parse-integer (nth 15 line))))
+ (let* ((cui (parse-ui (nth 0 line)))
+ (lui (parse-ui (nth 3 line)))
+ (sui (parse-ui (nth 5 line)))
+ (sab (nth 11 line))
+ (srl (parse-integer (nth 15 line)))
+ (srlus (srl-to-srlus srl)))
#+sbcl
(when (= 0 (mod (incf counter) 100000)) (sb-ext:gc :full t))
- ;; pfstr deprecated by KPKENG field in MRCONSO
+ ;; pfstr deprecated by KPFENG field in MRCONSO
#+nil
(unless (gethash cui pfstr-hash) ;; if haven't stored pfstr for cui
(when (and (string-equal (nth 1 line) "ENG") ; LAT
(set-lrl-hash lui srl lui-lrl-hash)
(set-lrl-hash sui srl sui-lrl-hash)
(set-lrl-hash (make-cuisui cui sui) srl cuisui-lrl-hash)
+ (set-lrl-hash cui srlus cui-lrlus-hash)
+ (set-lrl-hash lui srlus lui-lrlus-hash)
+ (set-lrl-hash sui srlus sui-lrlus-hash)
+ (set-lrl-hash (make-cuisui cui sui) srlus cuisui-lrlus-hash)
(multiple-value-bind (val found) (gethash sab sab-srl-hash)
(declare (ignore val))
(unless found
- (setf (gethash sab sab-srl-hash) srl))))))
+ (setf (gethash sab sab-srl-hash) srl)))
+ (multiple-value-bind (val found) (gethash sab sab-srlus-hash)
+ (declare (ignore val))
+ (unless found
+ (setf (gethash sab sab-srlus-hash) srlus))))))
(setq *preparse-hash-init?* t)
t)
#+nil (defun pfstr-hash (cui) (gethash cui pfstr-hash))
- (defun cui-lrl (cui) (gethash cui cui-lrl-hash))
- (defun lui-lrl (lui) (gethash lui lui-lrl-hash))
- (defun sui-lrl (sui) (gethash sui sui-lrl-hash))
- (defun sab-srl (sab) (aif (gethash sab sab-srl-hash) it 0))
+ (defun cui-lrl (cui) (gethash cui cui-lrl-hash))
+ (defun lui-lrl (lui) (gethash lui lui-lrl-hash))
+ (defun sui-lrl (sui) (gethash sui sui-lrl-hash))
(defun cuisui-lrl (cuisui) (gethash cuisui cuisui-lrl-hash))
+ (defun cui-lrlus (cui) (gethash cui cui-lrlus-hash))
+ (defun lui-lrlus (lui) (gethash lui lui-lrlus-hash))
+ (defun sui-lrlus (sui) (gethash sui sui-lrlus-hash))
+ (defun cuisui-lrlus (cuisui) (gethash cuisui cuisui-lrlus-hash))
+ (defun sab-srl (sab) (aif (gethash sab sab-srl-hash) it 0))
+ (defun sab-srlus (sab) (aif (gethash sab sab-srlus-hash) it 0))
)) ;; closure
-(defun set-lrl-hash (key lrl hash)
+
+(defun set-lrl-hash (key srl hash)
"Set the least restrictive level in hash table"
+ (declare (fixnum srl))
(multiple-value-bind (hash-lrl found) (gethash key hash)
- (if (or (not found) (< lrl hash-lrl))
- (setf (gethash key hash) lrl))))
+ (declare (type (or null fixnum) hash-lrl)
+ (boolean found))
+ (if (or (not found) (< srl hash-lrl))
+ (setf (gethash key hash) srl))))
;; UMLS file and column structures
;;; SQL datatypes symbols
;;; sql-u - Unique identifier
+;;; sql-t - Tiny integer (8-bit)
;;; sql-s - Small integer (16-bit)
;;; sql-i - Integer (32-bit)
;;; sql-l - Big integer (64-bit)
'(("AV" sql-f) ("BTS" sql-i) ("CLS" sql-i) ("COF" sql-i) ("CUI1" sql-u)
("AUI" sql-u) ("AUI1" sql-u) ("AUI2" sql-u) ("PCUI" sql-u)
("PLUI" sql-u) ("PAUI" sql-u) ("RUI" sql-u)
- ("CUI2" sql-u) ("CUI" sql-u) ("CXN" sql-s) ("FR" sql-i) ("LRL" sql-s)
+ ("CUI2" sql-u) ("CUI" sql-u) ("CXN" sql-s) ("FR" sql-i)
("LUI" sql-u) ("MAX" sql-s) ("MIN" sql-s) ("RANK" sql-s) ("REF" sql-c)
("PTR" sql-c)
- ("RNK" sql-s) ("RWS" sql-i) ("SRL" sql-s) ("SUI" sql-u) ("TUI" sql-u)
+ ("RNK" sql-s) ("RWS" sql-i) ("SRL" sql-t) ("SUI" sql-u) ("TUI" sql-u)
("MAPRANK" sql-s)
;;; Custom columns
- ("KCUISUI" sql-l) ("KCUILUI" sql-l) ("KCUILRL" sql-i) ("KLUILRL" sql-i)
- ("KSUILRL" sql-i)
- ("KSRL" sql-i) ("KLRL" sql-i)
+ ("KCUISUI" sql-l) ("KCUILUI" sql-l)
+ ("KSRL" sql-t) ("KSRLUS" sql-t) ("LRL" sql-t) ("LRLUS" sql-t)
+ ("KCUILRL" sql-t) ("KLUILRL" sql-t) ("KSUILRL" sql-t) ("KLRL" sql-t)
+ ("KCUILRLUS" sql-t) ("KLUILRLUS" sql-t) ("KSUILRLUS" sql-t) ("KLRLUS" sql-t)
;;; LEX columns
("EUI" sql-u) ("EUI2" sql-u)
;;; Semantic net columns
(lambda (x) (write-to-string (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 5 x))))))
("MRCONSO.RRF" "KCUILUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuilui (parse-ui (nth 0 x)) (parse-ui (nth 3 x))))))
- ("MRCONSO.RRF" "KCUILRL" "SMALLINT" 0
- (lambda (x) (write-to-string (lui-lrl (parse-ui (nth 0 x))))))
- ("MRCONSO.RRF" "KLUILRL" "SMALLINT" 0
+ ("MRCONSO.RRF" "KCUILRL" "TINYINT" 0
+ (lambda (x) (write-to-string (cui-lrl (parse-ui (nth 0 x))))))
+ ("MRCONSO.RRF" "KCUILRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cui-lrlus (parse-ui (nth 0 x))))))
+ ("MRCONSO.RRF" "KLUILRL" "TINYINT" 0
(lambda (x) (write-to-string (lui-lrl (parse-ui (nth 3 x))))))
- ("MRCONSO.RRF" "KSUILRL" "SMALLINT" 0
+ ("MRCONSO.RRF" "KLUILRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (lui-lrlus (parse-ui (nth 3 x))))))
+ ("MRCONSO.RRF" "KSUILRL" "TINYINT" 0
(lambda (x) (write-to-string (sui-lrl (parse-ui (nth 5 x))))))
- ("MRSTY.RRF" "KLRL" "SMALLINT" 0
+ ("MRCONSO.RRF" "KSUILRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sui-lrlus (parse-ui (nth 5 x))))))
+ ("MRCONSO.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (srl-to-srlus (parse-integer (nth 15 x))))))
+ ("MRSAB.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (srl-to-srlus (parse-integer (nth 3 x))))))
+ ("MRSTY.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string (cui-lrl (parse-ui (nth 0 x))))))
- ("MRCOC.RRF" "KLRL" "SMALLINT" 0
+ ("MRSTY.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cui-lrlus (parse-ui (nth 0 x))))))
+ ("MRCOC.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string
(max (cui-lrl (parse-ui (nth 0 x)))
(kmrcl:aif (cui-lrl (parse-ui (nth 1 x))) kmrcl::it 0)))))
- ("MRSAT.RRF" "KSRL" "SMALLINT" 0
+ ("MRCOC.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string
+ (max (cui-lrlus (parse-ui (nth 0 x)))
+ (kmrcl:aif (cui-lrl (parse-ui (nth 1 x))) kmrcl::it 0)))))
+ ("MRSAT.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 9 x)))))
- ("MRREL.RRF" "KSRL" "SMALLINT" 0
+ ("MRSAT.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 9 x)))))
+ ("MRREL.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 10 x)))))
- ("MRRANK.RRF" "KSRL" "SMALLINT" 0
+ ("MRREL.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 10 x)))))
+ ("MRRANK.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 1 x)))))
- ("MRHIER.RRF" "KSRL" "SMALLINT" 0
+ ("MRRANK.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 1 x)))))
+ ("MRHIER.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 4 x)))))
- ("MRMAP.RRF" "KSRL" "SMALLINT" 0
+ ("MRHIER.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 4 x)))))
+ ("MRMAP.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 1 x)))))
- ("MRSMAP.RRF" "KSRL" "SMALLINT" 0
+ ("MRMAP.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 1 x)))))
+ ("MRSMAP.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 1 x)))))
- ("MRDEF.RRF" "KSRL" "SMALLINT" 0
+ ("MRSMAP.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 1 x)))))
+ ("MRDEF.RRF" "KSRL" "TINYINT" 0
(lambda (x) (write-to-string (sab-srl (nth 4 x)))))
- #+nil ("MRCXT.RRF" "KSRL" "SMALLINT" 0 (lambda (x) (write-to-string (sab-srl (nth 2 x)))))
- ("MRXW_ENG.RRF" "KLRL" "SMALLINT" 0
+ ("MRDEF.RRF" "KSRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (sab-srlus (nth 4 x)))))
+ ("MRXW_ENG.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXW_NONENG.RRF" "KLRL" "SMALLINT" 0
+ ("MRXW_ENG.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
+ (parse-ui (nth 2 x))
+ (parse-ui (nth 4 x)))))))
+ ("MRXW_NONENG.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXNW_ENG.RRF" "KLRL" "SMALLINT" 0
+ ("MRXW_NONENG.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
+ (parse-ui (nth 2 x))
+ (parse-ui (nth 4 x)))))))
+ ("MRXNW_ENG.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXNS_ENG.RRF" "KLRL" "SMALLINT" 0
+ ("MRXNW_ENG.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
+ (parse-ui (nth 2 x))
+ (parse-ui (nth 4 x)))))))
+ ("MRXNS_ENG.RRF" "KLRL" "TINYINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
+ ("MRXNS_ENG.RRF" "KLRLUS" "TINYINT" 0
+ (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
+ (parse-ui (nth 2 x))
+ (parse-ui (nth 4 x)))))))
#+nil ("MRREL.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (nth 4 x)))))
#+nil ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (nth 2 x)))))
(defparameter +index-cols+
'(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
- ("SRL" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
+ ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
("SCUI" "MRCONSO")
("CUI" "MRDEF")
("SAB" "MRHIER")
#+ignore ("NSTR" "MRXNS_ENG" 10)
("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
- ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO") ("KCUILRL" "MRCONSO")
- ("KLUILRL" "MRCONSO")
+ ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO")
+ ("KCUILRL" "MRCONSO") ("KLUILRL" "MRCONSO") ("KSUILRL" "MRCONSO")
+ ("KCUILRLUS" "MRCONSO") ("KLUILRLUS" "MRCONSO") ("KSUILRLUS" "MRCONSO")
("KCUISUI" "MRSAT") ("KCUILUI" "MRSAT")
("KCUISUI" "MRXW_ENG") ("KCUISUI" "MRXNW_ENG")
("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
- ("KSRL" "MRDEF") ("KSRL" "MRRANK")
- ("KSRL" "MRREL") ("KSRL" "MRSAT") ("KLRL" "MRCOC")
- ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
+ ("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" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
+ ("KLRLUS" "MRXNS_ENG") ("KLRLUS" "MRXW_NONENG")
;; LEX indices
("EUI" "LRABR") ("EUI2" "LRABR") ("EUI" "LRAGR") ("EUI" "LRCMP") ("EUI" "LRMOD")
("EUI" "LRNOM") ("EUI2" "LRNOM") ("EUI" "LRPRN") ("EUI" "LRPRP") ("EUI" "LRSPL")
("STY_RL" "SRDEF") ("RT" "SRDEF") ("STY_RL" "SRSTR") ("STY_RL2" "SRSTR")
("RL" "SRSTR")
- ("SRL" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
+ ("SRL" "MRSAB") ("KSRLUS" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
("VCUI" "MRSAB") ("LAT" "MRSAB") ("MAPSETCUI" "MRMAP") ("MAPSETCUI" "MRSMAP")
("CUI" "MRHIER"))
"Columns in files to index")
projects / umlisp.git / commitdiff