+++ /dev/null
-;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp-orf -*-
-;;;; *************************************************************************
-;;;; 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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