-;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: composite.lisp
-;;;; Purpose: Composite Classes for UMLisp
-;;;; Programmer: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
-;;;;
-;;;; $Id: composite.lisp,v 1.3 2002/10/09 23:03:41 kevin Exp $
+;;;; Name: composite.lisp
+;;;; Purpose: Composite Classes for UMLisp
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2010 by Kevin M. Rosenberg, M.D.
;;;;
;;;; UMLisp users are granted the rights to distribute and use this software
;;;; as governed by the terms of the GNU General Public License.
;;;; *************************************************************************
-(in-package :umlisp)
-(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
-
+(in-package #:umlisp)
;;; Semantic type constants
(defun find-tui-word (words)
- (kmrcl:aif (car (find-usty-word words))
- (tui kmrcl::it)
+ (aif (car (find-usty-word words))
+ (tui it)
nil))
-(kmrcl:memoize 'find-tui-word)
+(memoize 'find-tui-word)
(defun tui-disease-or-syndrome ()
(find-tui-word "disease or syndrome"))
-(defun tui-sign-or-symptom ()
+(defun tui-sign-or-symptom ()
(find-tui-word "sign or symptom"))
(defun tui-finding ()
(find-tui-word "finding"))
(defun find-ucon2-tui (ucon tui cui2-func related-con-func)
"Returns a list of related ucons that have specific tui"
- (remove-duplicates
+ (remove-duplicates
(filter
- #'(lambda (c)
- (kmrcl:aif (funcall cui2-func c)
- (let ((ucon2 (find-ucon-cui kmrcl::it)))
- (when (ucon-is-tui? ucon2 tui)
- ucon2))
- nil))
+ #'(lambda (c)
+ (aif (funcall cui2-func c)
+ (let ((ucon2 (find-ucon-cui it)))
+ (when (ucon-is-tui? ucon2 tui)
+ ucon2)) nil))
(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))
-
+
(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 kmrcl: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 kmrcl: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 kmrcl: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 kmrcl: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)))
-
+(defclass freq (hyperobject)
+ ((freq :value-type integer :initarg :freq :accessor freq
+ :print-formatter fmt-comma-integer))
+ (:metaclass hyperobject-class)
+ (:default-initargs :freq 0)
+ (:user-name "Frequency class" "Frequency classes")
+ (:default-print-slots freq)
+ (:description "Base class containing frequency slot, used for multi-inherited objects"))
+
+(defclass ucon_freq (ucon freq)
+ ()
+ (:metaclass hyperobject-class)
+ (:user-name "Concept and Count" "Concepts and Counts")
+ (:default-print-slots cui freq pfstr)
+ (:description "Composite object of ucon/freq"))
+
+(defclass ustr_freq (ustr freq)
+ ()
+ (:metaclass hyperobject-class)
+ (:user-name "String and Count" "Strings and Counts")
+ (:default-print-slots sui freq stt lrl str)
+ (:description "Composite object of ustr/freq"))
+
+(defclass usty_freq (usty freq)
+ ()
+ (:metaclass hyperobject-class)
+ (:user-name "Semantic Type and Count" "Semantic Types and Counts")
+ (:default-print-slots tui freq sty)
+ (:description "Composite object of usty/freq"))
+
+(defun find-usty_freq-all ()
+ (let ((usty_freqs '()))
+ (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
+ (let* ((tui (car tuple))
+ (freq (ensure-integer
+ (caar (mutex-sql-query
+ (format nil "select count(*) from MRSTY where TUI=~a" tui)))))
+ (usty (find-usty-tui tui)))
+ (push (make-instance 'usty_freq :sty (sty usty)
+ :tui (tui usty) :freq freq) usty_freqs)))
+ (sort usty_freqs #'> :key #'freq)))
+
+
+(defclass usrl_freq (usrl freq)
+ ()
+ (:metaclass hyperobject-class)
+ (:user-name "Source and Count" "Sources and Counts")
+ (:default-print-slots sab freq srl)
+ (:description "Composite object of usrl/freq"))
;; 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))
- (kmrcl:aif (cui2 ucoc)
- (let ((ucon2 (find-ucon-cui kmrcl::it)))
+
+(defun find-usrl_freq-all ()
+ (let ((freqs '()))
+ (dolist (usrl (find-usrl-all))
+ (let ((freq (ensure-integer
+ (caar (mutex-sql-query
+ (format nil "select count(*) from MRSO where SAB='~a'"
+ (sab usrl)))))))
+ (push (make-instance 'usrl_freq :sab (sab usrl) :srl (srl usrl)
+ :freq freq)
+ freqs)))
+ (sort freqs #'> :key #'freq)))
+
+#+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))
+ (aif (cui2 ucoc)
+ (let ((ucon2 (find-ucon-cui it)))
(when (ucon-is-tui? ucon2 tui)
- (push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc))
- ucon_freqs)))))
+ (push (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
+ :pfstr (pfstr 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))))
+ (usty (car (find-usty-word sty))))
(if (and ucon usty)
- (funcall lookup-func ucon (tui usty))
+ (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))
(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
- (kmrcl:aif (aref ucon_freqs (cui ucon2))
- (setf (freq kmrcl::it) (1+ (freq kmrcl::it)))
- (setf (aref ucon_freqs (cui ucon2))
- (make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
+ (aif (aref ucon_freqs (cui ucon2))
+ (setf (freq it) (1+ (freq it)))
+ (setf (aref ucon_freqs (cui ucon2))
+ (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
+ :pfstr (pfstr ucon2) :freq 1)))))
(let ((ucon_freq-list '()))
(dotimes (i (find-cui-max))
- (declare (fixnum i))
- (kmrcl:awhen (aref ucon_freqs i)
- (push kmrcl::it ucon_freq-list)))
+ (declare (fixnum i))
+ (awhen (aref ucon_freqs i)
+ (push 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)
+#+mrcoc (defun find-ucon2_freq-coc-tui-all (tui)
(find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
+#+(or scl)
+(dolist (c '(ucon_freq ustr_freq usty_freq usrl_freq))
+ (let ((cl #+cmu (pcl:find-class c)
+ #+scl (find-class c)))
+ #+cmu (pcl:finalize-inheritance cl)
+ #+scl (clos:finalize-inheritance cl)))
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