Common Lisp Package: UMLISP-USER

User package for UMLisp

README:

FUNCTION

Public

CUI-P (UI)

Check if a string is a CUI

ENGLISH-TERM-P (OBJ)

Returns two values: T/NIL if term is english and T/NIL if obj is a TERM

FIND-CUI-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of cui that match word, optionally use SQL's LIKE syntax

FIND-CUI-UCON-ALL (&KEY (SRL *CURRENT-SRL*))

Return list of CUIs for all ucons

FIND-CUI2-UREL-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Return a list of urel for cui

FIND-LUI-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of cui that match word, optionally use SQL's LIKE syntax

FIND-PFSTR-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Find preferred string for a cui

FIND-STRING-SUI (SUI &KEY (SRL *CURRENT-SRL*))

Return the string associated with sui

FIND-SUI-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of cui that match word, optionally use SQL's LIKE syntax

FIND-UCOC-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Return a list of ucoc for cui

FIND-UCOC-CUI2 (CUI2 &KEY (SRL *CURRENT-SRL*))

Return a list of ucoc for cui2

FIND-UCON-ALL (&KEY (SRL *CURRENT-SRL*))

Return list of all ucon's

FIND-UCON-AUI (AUI &KEY (SRL *CURRENT-SRL*))

Find list of ucon for aui

FIND-UCON-COC-CUI2 (CUI2 &KEY (SRL *CURRENT-SRL*))

List of ucon with co-occurance cui2

FIND-UCON-CUI (CUI &KEY (SRL *CURRENT-SRL*) WITHOUT-PFSTR)

Find ucon for a cui. If set SAB, the without-pfstr is on by default

FIND-UCON-CUI-SUI (CUI SUI &KEY (SRL *CURRENT-SRL*))

Find ucon for cui/sui

FIND-UCON-CUISUI (CUISUI &KEY (SRL *CURRENT-SRL*))

Find ucon for cui/sui

FIND-UCON-LUI (LUI &KEY (SRL *CURRENT-SRL*))

Find list of ucon for lui

FIND-UCON-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of ucons that match word, optionally use SQL's LIKE syntax

FIND-UCON-STR (STR &KEY (SRL *CURRENT-SRL*))

Find ucon that are exact match for str

FIND-UCON-SUI (SUI &KEY (SRL *CURRENT-SRL*))

Find list of ucon for sui

FIND-UCON-TUI (TUI &KEY (SRL *CURRENT-SRL*))

Find list of ucon for tui

FIND-UCON-WORD (WORD &KEY SAB (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of ucon that match word in matching SAB. Optionally, use SQL's LIKE syntax

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-COC-TUI (UCON TUI)

Return list of ucon's that have co-occuring concepts of semantic type tui

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-REL-TUI (UCON TUI)

Return list of ucon's that have related concepts to ucon and semantic type tui

FIND-UCON2-STR&STY (STR STY LOOKUP-FUNC)

Call lookup-func for ucon and usty for given str and sty

FIND-UCON2-TUI (UCON TUI CUI2-FUNC RELATED-CON-FUNC)

Returns a list of related ucons that have specific tui

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

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 UCON2-TUI-FUNC)

Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui

FIND-UCONSO-CODE (CODE &KEY FIRST SAB (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of uconso objects that match code. Optional, filter for SAB. Optionally, use SQL's LIKE syntax

FIND-UCONSO-CUI (CUI &KEY SAB (SRL *CURRENT-SRL*))

Find uconso for a cui.

FIND-UCONSO-CUISUI (CUISUI &KEY SAB (SRL *CURRENT-SRL*))

Find uconso for a cuisui.

FIND-UCONSO-SUI (SUI &KEY SAB (SRL *CURRENT-SRL*))

Find uconso for a sui. If set SAB, the without-pfstr is on by default

FIND-UCONSO-WORD (WORD &KEY SAB (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of uconso that match word. Optionally, matching SAB. Optionally, use SQL's LIKE syntax

FIND-UDEF-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Return a list of udefs for cui

FIND-UDOC-KEY (KEY)

Return list of abbreviation documentation for a key

FIND-UDOC-VALUE (VALUE)

Return abbreviation documentation

FIND-UREL-CUI (CUI &KEY (SRL *CURRENT-SRL*) FILTER WITHOUT-PFSTR2)

Return a list of urel for cui

FIND-UREL-CUI2 (CUI2 &KEY (SRL *CURRENT-SRL*))

Return a list of urel for cui2

FIND-USAB-ALL

Return all usab objects

FIND-USAB-RSAB (RSAB &KEY (CURRENT T))

Find usab for rsab

FIND-USAB-VSAB (VSAB &KEY (CURRENT T))

Find usab for vsab

FIND-USTR-ALL (&KEY (SRL *CURRENT-SRL*))

Return list of all ustr's

FIND-USTR-CUI-SUI (CUI SUI &KEY (SRL *CURRENT-SRL*))

Return the single ustr for cuisui

FIND-USTR-CUILUI (CUI LUI &KEY (SRL *CURRENT-SRL*))

Return a list of ustr for cui/lui

FIND-USTR-CUISUI (CUISUI &KEY (SRL *CURRENT-SRL*))

Return the single ustr for cuisui

FIND-USTR-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*))

Return list of ustrs that match word

FIND-USTR-SAB (SAB &KEY (SRL *CURRENT-SRL*))

Return the list of ustr for sab

FIND-USTR-SUI (SUI &KEY (SRL *CURRENT-SRL*))

Return the list of ustr for sui

FIND-USTR-WORD (WORD &KEY SAB (SRL *CURRENT-SRL*) (LIKE NIL))

Return list of ustr that match word in matching SAB. Optionally, use SQL's LIKE syntax

FIND-USTY-ALL

Return list of usty's for all semantic types

FIND-USTY-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Return a list of usty for cui

FIND-USTY-STY (STY)

Find usty for a sty

FIND-USTY-TUI (TUI)

Find usty for tui

FIND-USTY-WORD (WORD &KEY (SRL *CURRENT-SRL*))

Return a list of usty that match word

FIND-UTERM-CUI (CUI &KEY (SRL *CURRENT-SRL*))

Return a list of uterm for cui

FIND-UTERM-CUILUI (CUI LUI &KEY (SRL *CURRENT-SRL*))

Return single uterm for cui/lui

FIND-UTERM-LUI (LUI &KEY (SRL *CURRENT-SRL*))

Return a list of uterm for lui

FIND-UTERM-NORMALIZED-WORD (WORD &KEY (SRL *CURRENT-SRL*))

Return list of uterms that match word

FIND-UTERM-WORD (WORD &KEY (SRL *CURRENT-SRL*))

Return list of uterms that match word

LUI-P (UI)

Check if a string is a LUI

MAP-UCON-ALL (FN &KEY (SRL *CURRENT-SRL*))

Map a function over all ucon's

SQL-DISCONNECT (CONN)

Disconnect from UMLS database, but put connection back into pool

SUI-P (UI)

Check if a string is a SUI

UCON-HAS-TUI (UCON TUI)

Returns T if UCON has a semantic type of TUI.

UCON-IS-TUI? (UCON TUI)

Returns t if ucon has a semantic type of tui

UCON-USTRS (UCON)

Return lists of strings for a concept

Undocumented

CURRENT-SRL

DISPLAY-CON (KEYVAL &KEY (STREAM *STANDARD-OUTPUT*) (VID COMPACT-TEXT) (FILE-WRAPPER T) (ENGLISH-ONLY NIL) (SUBOBJECTS NIL))

DISPLAY-STR (KEYVAL &KEY (STREAM *STANDARD-OUTPUT*) (VID COMPACT-TEXT) (FILE-WRAPPER T) (ENGLISH-ONLY NIL) (SUBOBJECTS NIL))

DISPLAY-TERM (KEYVAL &KEY (STREAM *STANDARD-OUTPUT*) (VID COMPACT-TEXT) (FILE-WRAPPER T) (ENGLISH-ONLY NIL) (SUBOBJECTS NIL))

EUI-P (UI)

FILTER-URELS-BY-REL (URELS REL &KEY (REMOVE-DUPLICATE-PFSTR2 T) (SORT PFSTR2))

FIND-CUI-MAX

FIND-LABR-BAS (BAS)

FIND-LABR-EUI (EUI)

FIND-LAGR-EUI (EUI)

FIND-LCMP-EUI (EUI)

FIND-LEXTERM-EUI (EUI)

FIND-LEXTERM-WORD (WRD)

FIND-LMOD-EUI (EUI)

FIND-LNOM-EUI (EUI)

FIND-LPRN-EUI (EUI)

FIND-LPRP-EUI (EUI)

FIND-LSPL-EUI (EUI)

FIND-LTRM-EUI (EUI)

FIND-LTYP-EUI (EUI)

FIND-LWD-WRD (WRD)

FIND-SDEF-UI (UI)

FIND-SSTR-RL (RL)

FIND-SSTR-STYRL (STYRL)

FIND-SSTRE1-UI (UI)

FIND-SSTRE1-UI2 (UI2)

FIND-UCON-MULTIWORD (STR &KEY (SRL *CURRENT-SRL*) (ONLY-EXACT-IF-MATCH T) LIMIT SAB)

FIND-UCON-REL-CUI2 (CUI2 &KEY (SRL *CURRENT-SRL*))

FIND-UCON2_FREQ-COC-TUI-ALL (TUI)

FIND-UCONSO-MULTIWORD (STR &KEY (SRL *CURRENT-SRL*) (ONLY-EXACT-IF-MATCH T) LIMIT SAB)

FIND-UDOC-KEY-VALUE (DOCKEY VALUE)

FIND-USAT-UI (CUI &OPTIONAL LUI SUI &KEY (SRL *CURRENT-SRL*))

FIND-USO-AUI (AUI &KEY (SRL *CURRENT-SRL*))

FIND-USO-CUI (CUI &KEY (SRL *CURRENT-SRL*) (ENGLISH-ONLY NIL) LIMIT)

FIND-USO-CUISUI (CUI SUI &KEY (SRL *CURRENT-SRL*))

FIND-USRL-ALL

FIND-USRL_FREQ-ALL

FIND-USTATS-ALL (&KEY (SRL *CURRENT-SRL*))

FIND-USTATS-SRL (SRL)

FIND-USTR-IN-UCON (UCON SUI)

FIND-USTR-IN-UTERM (UTERM SUI)

FIND-USTR-MULTIWORD (STR &KEY (SRL *CURRENT-SRL*) (ONLY-EXACT-IF-MATCH T) LIMIT SAB)

FIND-USTY_FREQ-ALL

FIND-UTERM-IN-UCON (UCON LUI)

FIND-UTERM-MULTIWORD (STR &KEY (SRL *CURRENT-SRL*) (ONLY-EXACT-IF-MATCH T) LIMIT)

LAT-ABBR-INFO (LAT)

MAKE-UCON-CUI (CUI)

PARSE-CUI (CUI)

PARSE-EUI (EUI)

PARSE-LUI (LUI)

PARSE-SUI (SUI)

PARSE-TUI (TUI)

REL-ABBR-INFO (REL)

REMOVE-ENGLISH-TERMS (UTERMS)

REMOVE-NON-ENGLISH-TERMS (UTERMS)

SET-CURRENT-SRL (SRL)

SET-UMLS-PATH (P)

SET-UMLS-SQL-DB (DB)

SET-UMLS-SQL-HOST (H)

SET-UMLS-SQL-PASSWD (P)

SET-UMLS-SQL-TYPE (H)

SET-UMLS-SQL-USER (U)

SQL-DISCONNECT-POOLED

STT-ABBR-INFO (STT)

TUI-DISEASE-OR-SYNDROME

TUI-FINDING

TUI-P (UI)

TUI-SIGN-OR-SYMPTOM

UCON-HAS-SAB (UCON SAB)

UMLS-SQL-DB

UMLS-SQL-HOST

UMLS-SQL-PASSWD

UMLS-SQL-TYPE

UMLS-SQL-USER

USO-UNIQUE-CODES (USOS)

MACRO

Public

Undocumented

WITH-SQL-CONNECTION ((CONN) &BODY BODY)

GENERIC-FUNCTION

Public

Undocumented

FMT-AUI (AUI)

FMT-CUI (C)

FMT-EUI (E)

FMT-LUI (C)

FMT-SUI (S)

FMT-TUI (TUI)

MESH-NUMBER (OBJ)

PF-USTR (OBJ)

SLOT-ACCESSOR

Public

PFSTR (OBJECT)

Return the preferred string for a ustr, which is the string itself

Undocumented

ATN (OBJECT)

ATV (OBJECT)

AUI (OBJECT)

BAS (OBJECT)

BAS2 (OBJECT)

COA (OBJECT)

CODE (OBJECT)

COF (OBJECT)

COT (OBJECT)

CUI (OBJECT)

CUI1 (OBJECT)

CUI2 (OBJECT)

CUILIST (OBJECT)

CVF (OBJECT)

DEF (OBJECT)

DOCKEY (OBJECT)

DTYPE (OBJECT)

DVALUE (OBJECT)

EUI (OBJECT)

EUI2 (OBJECT)

EXPL (OBJECT)

HCD (OBJECT)

IMETA (OBJECT)

ISPREF (OBJECT)

KPFENG (OBJECT)

LAT (OBJECT)

LRL (OBJECT)

LUI (OBJECT)

NSTR (OBJECT)

PFSTR2 (OBJECT)

RANK (OBJECT)

RCUI (OBJECT)

REL (OBJECT)

RELA (OBJECT)

RL (OBJECT)

RMETA (OBJECT)

RSAB (OBJECT)

RUI (OBJECT)

S#COC (OBJECT)

S#DEF (OBJECT)

S#REL (OBJECT)

S#SAT (OBJECT)

S#SO (OBJECT)

S#STR (OBJECT)

S#STY (OBJECT)

S#TERM (OBJECT)

SAB (OBJECT)

SAUI (OBJECT)

SCC (OBJECT)

SCIT (OBJECT)

SCUI (OBJECT)

SDUI (OBJECT)

SL (OBJECT)

SLC (OBJECT)

SRL (OBJECT)

STR (OBJECT)

STT (OBJECT)

STY (OBJECT)

STY2 (OBJECT)

SUI (OBJECT)

SUPPRESS (OBJECT)

TS (OBJECT)

TTY (OBJECT)

TUI (OBJECT)

UI (OBJECT)

UI2 (OBJECT)

UI3 (OBJECT)

UN (OBJECT)

VCUI (OBJECT)

VSAB (OBJECT)

WD (OBJECT)

VARIABLE

Public

Undocumented

*CURRENT-SRL*

*UMLS-SQL-DB*

CLASS

Public

Undocumented

LABR

LAGR

LCMP

LEXTERM

LMOD

LNOM

LPRN

LPRP

LSPL

LTRM

LTYP

LWD

SDEF

SSTR

SSTRE1

SSTRE2

UCOC

UCON

UCON_FREQ

UDEF

UDOC

UMLSCLASS

URANK

UREL

USAB

USAT

USO

USRL

USRL_FREQ

USTR

USTR_FREQ

USTY

USTY_FREQ

UTERM

UXNS

UXNW

UXW