--- /dev/null
+;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: composite.lisp
+;;;; Purpose: Composite Classes for UMLisp
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
+;;;;
+;;;; $Id$
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2004 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-orf)
+
+;;; Semantic type constants
+
+(defun find-tui-word (words)
+ (aif (car (find-usty-word words))
+ (tui it)
+ nil))
+(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)
+ (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)
+ "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 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-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)))
+
+(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 :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))))
+ (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
+ (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))
+ (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)
+ (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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