1 ;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
5 ;;;; Name: composite.lisp
6 ;;;; Purpose: Composite Classes for UMLisp
7 ;;;; Programmer: Kevin M. Rosenberg
8 ;;;; Date Started: Apr 2000
10 ;;;; $Id: composite.lisp,v 1.17 2002/12/09 14:11:09 kevin Exp $
12 ;;;; This file, part of UMLisp, is
13 ;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
15 ;;;; UMLisp users are granted the rights to distribute and use this software
16 ;;;; as governed by the terms of the GNU General Public License.
17 ;;;; *************************************************************************
20 (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
23 ;;; Semantic type constants
25 (defun find-tui-word (words)
26 (aif (car (find-usty-word words))
29 (memoize 'find-tui-word)
31 (defun tui-disease-or-syndrome ()
32 (find-tui-word "disease or syndrome"))
33 (defun tui-sign-or-symptom ()
34 (find-tui-word "sign or symptom"))
36 (find-tui-word "finding"))
39 ;;;; Related concepts with specific tui lookup functions
41 (defun ucon-is-tui? (ucon tui)
42 "Returns t if ucon has a semantic type of tui"
43 (find tui (s#sty ucon) :key #'tui))
45 (defun find-ucon2-tui (ucon tui cui2-func related-con-func)
46 "Returns a list of related ucons that have specific tui"
50 (aif (funcall cui2-func c)
51 (let ((ucon2 (find-ucon-cui it)))
52 (when (ucon-is-tui? ucon2 tui)
55 (funcall related-con-func ucon))
58 (defun find-ucon2-coc-tui (ucon tui)
59 "Return list of ucon's that have co-occuring concepts of semantic type tui"
60 (find-ucon2-tui ucon tui #'cui2 #'s#coc))
62 (defun find-ucon2-rel-tui (ucon tui)
63 "Return list of ucon's that have related concepts to ucon and semantic type tui"
64 (find-ucon2-tui ucon tui #'cui2 #'s#rel))
68 (defclass freq (hyperobject)
69 ((freq :type integer :initarg :freq :accessor freq :print-formatter fmt-comma-integer))
70 (:metaclass hyperobject-class)
71 (:default-initargs :freq 0)
72 (:user-name "Frequency class")
74 (:description "Base class containing frequency slot, used for multi-inherited objects"))
76 (defclass ucon_freq (ucon freq)
78 (:metaclass hyperobject-class)
79 (:user-name "Concept and Count")
80 (:print-slots cui freq pfstr)
81 (:description "Composite object of ucon/freq"))
83 (defclass ustr_freq (ustr freq)
85 (:metaclass hyperobject-class)
86 (:user-name "String and Count")
87 (:print-slots sui freq stt lrl str)
88 (:description "Composite object of ustr/freq"))
90 (defclass usty_freq (usty freq)
91 ((freq :type fixnum :initarg :freq :accessor freq))
92 (:metaclass hyperobject-class)
93 (:user-name "Semantic Type and Count")
94 (:print-slots tui freq sty)
95 (:description "Composite object of usty/freq"))
97 (defun find-usty_freq-all ()
98 (let ((usty_freqs '()))
99 (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
100 (let* ((tui (car tuple))
101 (freq (ensure-integer
102 (caar (mutex-sql-query
103 (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
104 (push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
105 (sort usty_freqs #'> :key #'freq)))
108 (defclass usrl_freq (usrl freq)
110 (:metaclass hyperobject-class)
111 (:user-name "Source and Count")
112 (:print-slots sab freq srl)
113 (:description "Composite object of usrl/freq"))
115 ;; Frequency finding functions
117 (defun find-usrl_freq-all ()
119 (dolist (usrl (find-usrl-all))
120 (let ((freq (ensure-integer
121 (caar (mutex-sql-query
122 (format nil "select count(*) from MRSO where SAB='~a'"
124 (push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
125 (sort freqs #'> :key #'freq)))
127 (defun find-ucon2_freq-coc-tui (ucon tui)
128 "Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui"
129 (let ((ucon_freqs '()))
130 (dolist (ucoc (s#coc ucon))
132 (let ((ucon2 (find-ucon-cui it)))
133 (when (ucon-is-tui? ucon2 tui)
134 (push (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
135 :pfstr (pfstr ucon2) :freq (cof ucoc))
137 (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
138 (sort ucon_freqs #'> :key #'freq)))
140 (defun find-ucon2-str&sty (str sty lookup-func)
141 "Call lookup-func for ucon and usty for given str and sty"
142 (let ((ucon (car (find-ucon-str str)))
143 (usty (car (find-usty-word sty))))
145 (funcall lookup-func ucon (tui usty))
148 (defun find-ucon2-coc-str&sty (str sty)
149 "Find all ucons that are a co-occuring concept for concept named str
150 and that have semantic type of sty"
151 (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))
153 (defun find-ucon2-rel-str&sty (str sty)
154 "Find all ucons that are a relationship to concept named str
155 and that have semantic type of sty"
156 (find-ucon2-str&sty str sty #'find-ucon2-rel-tui))
158 ;;; Most common relationships, co-occurances
160 (defun find-ucon2_freq-tui-all (tui ucon2-tui-func)
161 "Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui"
162 (let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
163 (dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
164 (dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
165 (aif (aref ucon_freqs (cui ucon2))
166 (setf (freq it) (1+ (freq it)))
167 (setf (aref ucon_freqs (cui ucon2))
168 (make-instance 'ucon_freq :cui (cui ucon2) :lrl (lrl ucon2)
169 :pfstr (pfstr ucon2) :freq 1)))))
170 (let ((ucon_freq-list '()))
171 (dotimes (i (find-cui-max))
173 (awhen (aref ucon_freqs i)
174 (push it ucon_freq-list)))
175 (sort ucon_freq-list #'> :key #'freq))))
177 (defun find-ucon2_freq-rel-tui-all (tui)
178 "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
179 (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))
181 (defun find-ucon2_freq-coc-tui-all (tui)
182 (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
185 (dolist (c '(ucon_freq ustr_freq usty_freq usrl_freq))
186 (let ((cl #+cmu (pcl:find-class c)
187 #+scl (find-class c)))
188 #+cmu (pcl:finalize-inheritance cl)
189 #+scl (clos:finalize-inheritance cl)))