+++ /dev/null
-;;;; $Id: obj-composite.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
-
-(in-package :umlisp)
-
-
-;;; Semantic type constants
-
-(defun find-tui-word (words)
- (gu:aif (car (find-usty-word words))
- (tui gu::it)
- nil))
-(gu:memoize 'find-tui-word)
-
-(defun tui-disease-or-syndrome ()
- (find-tui-word "disease or syndrome"))
-(defun tui-sign-or-symptom ()
- (find-tui-word "sign or symptom"))
-(defun tui-finding ()
- (find-tui-word "finding"))
-
-
-;;;; Related concepts with specific tui lookup functions
-
-(defun ucon-is-tui? (ucon tui)
- "Returns t if ucon has a semantic type of tui"
- (find tui (s#sty ucon) :key #'tui))
-
-(defun find-ucon2-tui (ucon tui cui2-func related-con-func)
- "Returns a list of related ucons that have specific tui"
- (remove-duplicates
- (filter
- #'(lambda (c)
- (gu:aif (funcall cui2-func c)
- (let ((ucon2 (find-ucon-cui gu::it)))
- (when (ucon-is-tui? ucon2 tui)
- ucon2))
- nil))
- (funcall related-con-func ucon))
- :key #'cui))
-
-(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))
-
-(defun find-ucon2-rel-tui (ucon tui)
- "Return list of ucon's that have related concepts to ucon and semantic type tui"
- (find-ucon2-tui ucon tui #'cui2 #'s#rel))
-
-;;; Composite Objects
-
-(defclass ucon_freq (umlsclass)
- ((ucon :type ucon :initarg :ucon :reader ucon)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :cui nil :pfstr nil :freq nil)
- (:title "Concept and Count")
- (:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
- (:ref-fields (cui find-ucon-cui))
- (:documentation "Composite object of ucon/freq"))
-
-(defun ucon_freq-cui (c)
- (cui (ucon c)))
-
-(defun ucon_freq-pfstr (c)
- (pfstr (ucon c)))
-
-(defclass ustr_freq (umlsclass)
- ((ustr :type ustr :initarg :ustr :reader ustr)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :cui nil :pfstr nil :freq nil)
- (:title "String and Count")
- (:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
- (:ref-fields (sui find-ustr-sui))
- (:documentation "Composite object of ustr/freq"))
-
-(defun ustr_freq-sui (s)
- (sui (ustr s)))
-
-(defun ustr_freq-str (s)
- (str (ustr s)))
-
-(defun ustr_freq-lrl (s)
- (lrl (ustr s)))
-
-(defun ustr_freq-stt (s)
- (stt (ustr s)))
-
-(defclass usty_freq (umlsclass)
- ((usty :type usty :initarg :usty :reader usty)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :usty nil :freq nil)
- (:title "Semantic Type and Count")
- (:ref-fields (tui find-ucon-tui "subobjects=no"))
- (:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
- (:documentation "Composite object of usty/freq"))
-
-(defun usty_freq-tui (s)
- (tui (usty s)))
-
-(defun usty_freq-sty (s)
- (sty (usty s)))
-
-(defclass usrl_freq (umlsclass)
- ((usrl :type usrl :initarg :usrl :reader usrl)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :usrl nil :freq nil)
- (:title "Source and Count")
- (:ref-fields (sab find-ustr-sab))
- (:fields (sab :string) (freq :commainteger) (srl :fixnum))
- (:documentation "Composite object of usrl/freq"))
-
-(defun usrl_freq-sab (s)
- (sab (usrl s)))
-
-(defun usrl_freq-srl (s)
- (srl (usrl s)))
-
-
-;; Frequency finding functions
-(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))
- (gu:aif (cui2 ucoc)
- (let ((ucon2 (find-ucon-cui gu::it)))
- (when (ucon-is-tui? ucon2 tui)
- (push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc))
- ucon_freqs)))))
- (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
- (sort ucon_freqs #'> :key #'freq)))
-
-(defun find-ucon2-str&sty (str sty lookup-func)
- "Call lookup-func for ucon and usty for given str and sty"
- (let ((ucon (car (find-ucon-str str)))
- (usty (car (find-usty-word sty))))
- (if (and ucon usty)
- (funcall lookup-func ucon (tui usty))
- nil)))
-
-(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))
-
-(defun find-ucon2-rel-str&sty (str sty)
- "Find all ucons that are a relationship to concept named str
- and that have semantic type of sty"
- (find-ucon2-str&sty str sty #'find-ucon2-rel-tui))
-
-;;; Most common relationships, co-occurances
-
-(defun find-ucon2_freq-tui-all (tui ucon2-tui-func)
- "Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui"
- (let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
- (dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
- (dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
- (gu:aif (aref ucon_freqs (cui ucon2))
- (setf (freq gu::it) (1+ (freq gu::it)))
- (setf (aref ucon_freqs (cui ucon2))
- (make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
- (let ((ucon_freq-list '()))
- (dotimes (i (find-cui-max))
- (declare (fixnum i))
- (gu:awhen (aref ucon_freqs i)
- (push gu::it ucon_freq-list)))
- (sort ucon_freq-list #'> :key #'freq))))
-
-(defun find-ucon2_freq-rel-tui-all (tui)
- "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)
- (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
-
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