Common Lisp Package: 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)

Private

ADD-UCOLS (UCOLS)

Adds a ucol or list of ucols to *umls-cols*. Returns input value.

ADD-UFILES (UFILES)

Adds a ufile or list of ufiles to *umls-filess*. Returns input value.

CREATE-ALL-TABLES-CMDFILE

Return sql commands to create all tables. Not need for automated SQL import

CREATE-CUSTOM-TABLE-CMD (TABLENAME SQL-CMD)

Return SQL command to create a custom table

CREATE-INDEX-CMD (COLNAME TABLENAME LENGTH)

Return sql create index command

CREATE-TABLE-CMD (FILE)

Return sql command to create a table

CREATE-UMLS-DB (&KEY (EXTENSION -trans) (FORCE-TRANSLATION NIL) (VERBOSE NIL))

SQL Databases: initializes entire database via SQL copy commands. This is much faster that using create-umls-db-insert.

CREATE-UMLS-DB-BY-INSERT (&KEY VERBOSE)

SQL Databases: initializes entire database via SQL insert commands

CUSTOM-COL-VALUES (UCOLS VALUES DOQUOTE)

Returns a list of string column values for SQL inserts for custom columns

DATATYPE-FOR-COLNAME (COLNAME)

Return datatype for column name

DECOMPOSE-CUISUI (CUISUI)

Returns the CUI and SUI of a cuisui number

DROP-INDEX-CMD (COLNAME TABLENAME)

Return sql create index command

ENGLISH-TERM-FILTER (OBJ)

Retrns NIL if object is a term and not english

ENSURE-COMPILED-FUN (FUN)

Ensure that a function is compiled

ENSURE-FIELD-LENGTHS

Initial colstruct field lengths for files that don't have a measurement. Currently, these are the LEX and NET files.

ENSURE-UCOL-DATATYPE (COL DATATYPE)

Add data type information to column

ENSURE-UCOLS+UFILES (&OPTIONAL (ALWAYSCLEAR NIL))

Initialize all UMLS file and column structures if not already initialized

FILE-FIELD-LENGTHS (UFILE)

Returns a list of FILENAME MAX AV

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

Find LRL for a cui

FIND-UCOL (COLNAME FILENAME)

Returns list of umls-col structure for a column name and a filename

FIND-UCOL-OF-COLNAME (COLNAME FILENAME UCOLS)

Returns list of umls-col structure for a column name and a filename

FIND-UCOLS-FOR-UFILE (UFILE)

Returns list of umls-cols for a file structure

FIND-UCON-ALL2 (&KEY (SRL *CURRENT-SRL*))

Return list of all ucon's

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

Return list of ucons that match non-english word

FIND-UDOC-ALL

Return all abbreviation documentation

FIND-UFILE (FILENAME)

Returns umls-file structure for a filename

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

Return the urel for a rui

FIND-USAB-BY-KEY (KEY-NAME KEY &KEY CURRENT)

Find usab for a key

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

Return list of ustrs that match non-english word

GEN-UCOLS-CUSTOM

Initialize umls columns for custom columns

GEN-UCOLS-GENERIC (COL-FILENAME)

Initialize for generic (LEX/NET) columns

GEN-UCOLS-META

Initialize all umls columns

GEN-UFILES-GENERIC (FILES-FILENAME DIR)

Initialize generic UMLS file structures

INSERT-VALUES-CMD (FILE VALUES)

Return sql insert command for a row of values

MAKE-NONENG-INDEX-FILE (EXTENSION &KEY FORCE)

Make non-english index file

MAX-UMLS-FIELD

Return length of longest field

MAX-UMLS-ROW

Return length of longest row

MYSQL-COPY-CMD (FILE EXTENSION &KEY (LOCAL-FILE T))

Return mysql copy statement for a file

PARSE-UI (S &OPTIONAL (NULLVALUE 0))

Return integer value for a UMLS unique identifier.

PG-COPY-CMD (FILE EXTENSION)

Return postgresql copy statement for a file

POSITION-FIELD-FILE (FILENAME FIELDNAME)

Returns the position of a field in a file

READ-UMLS-LINE (STRM &OPTIONAL (EOF 'EOF))

Read a line from a UMLS stream, split into fields

REMOVE-CUSTOM-COLS (COLS)

Remove custom cols from a list col umls-cols

SET-LRL-HASH (KEY SRL HASH)

Set the least restrictive level in hash table

SORT-SCORE-PFSTR-STR (STR UOBJS)

Return list of sorted and scored ucons. Score by match of str to ucon-pfstr

SORT-SCORE-UMLSCLASS-STR (OBJS STR LOOKUP-FUNC)

Sort a list of objects based on scoring to a string

SORT-SCORE-USTR-STR (STR USTRS)

Return list of sorted and scored ucons. Score by match of str to ucon-pfstr

SQL-CONNECT

Connect to UMLS database, automatically used pooled connections

SQL-CREATE-CUSTOM-TABLES (CONN)

SQL Databases: create all custom tables

SQL-CREATE-INDEXES (CONN &KEY (INDEXES +INDEX-COLS+) VERBOSE)

SQL Databases: create all indexes

SQL-CREATE-TABLES (CONN)

SQL Databases: create all tables

SQL-DROP-TABLES (CONN)

SQL Databases: drop all tables

SQL-INSERT-ALL-VALUES (CONN)

SQL Databases: inserts all values for all files

SQL-INSERT-VALUES (CONN FILE)

SQL Databases: inserts all values for a file

SRL-TO-SRLUS (SRL)

Convert the standard SRL category to one oriented for use in the ~ United States. Specifically, SRL 4 in the USA has license restrictions ~ between SRL 1 and 2 when used in the United States. As of 2009AA, the SNOMED SRL changed from 4 to 9. So we create a new scale ~ (SRLUS) where SRL to SRLUS mapping is: ~ (0->0, 1->1, 4->2, 9->2, 2->3, 3->4).

TRANSLATE-ALL-FILES (&KEY (EXTENSION -trans) VERBOSE FORCE)

Translate all *umls-files* to optimized import format.

TRANSLATE-FILES (OUT-UFILE EXTENSION INPUT-UFILES &KEY FORCE)

Translate a umls file into a format suitable for sql copy cmd

TRANSLATE-LINE (FILE LINE STRM)

Translate a single line for sql output

TRANSLATE-UMLS-FILE (FILE EXTENSION &KEY FORCE)

Translate a umls file into a format suitable for sql copy cmd

UFILE-PATHNAME (UFILE &OPTIONAL (EXTENSION ))

Return pathname for a umls filename with an optional extension

UFILES-FIELD-LENGTHS (UFILES)

Returns a list of lists of containing (FILE MAX AV)

UFILES-TO-MEASURE

Returns a list of ufiles to measure

UMLS-FIELD-STRING-TO-LIST (FMT)

Converts a comma delimited list of fields into a list of field names. Will append a unique number (starting at 2) onto a column name that is repeated in the list

UMLS-FIXED-SIZE-WASTE

Display storage waste if using all fixed size storage

UMLS-PATHNAME (FILENAME &OPTIONAL (EXTENSION ))

Return pathname for a umls filename with an optional extension

VERIFY-TRANSLATION-FILE (OUTPUT-PATH INPUT-UFILES)

Returns t if translation file exists and is correct size. Warns and deletes incomplete translation file.

Undocumented

CANONICALIZE-COLUMN-TYPE (TYPE)

CHECK-UI (UI START-CHAR LEN)

CLEAR-PREPARSE-HASH-TABLES

COPY-OR-NEW-UCOL (COLNAME FILENAME UCOL)

CUI-LRL (CUI)

CUI-LRLUS (CUI)

CUISUI-LRL (CUISUI)

CUISUI-LRLUS (CUISUI)

CUSTOM-COL-VALUE (COL VALUES DOQUOTE)

CUSTOM-COLNAMES-FOR-FILENAME (FILENAME)

CUSTOM-UCOLS-FOR-FILE (FILE)

DECOMPOSE-FIL (FIL)

DISPLAY-WASTE

ENSURE-COL-IN-COLUMNS (COLNAME FILENAME UCOLS)

ENSURE-PREPARSE (&OPTIONAL (FORCE-READ NIL))

ESCAPE-COLUMN-NAME (NAME)

FILENAME-TO-TABLENAME (FILE)

FILTER-UCOCS (UCOCS &KEY (REMOVE-DUPLICATE-PFSTR2 T) (SORT PFSTR2))

FIND-COUNT-TABLE (CONN TABLE SRL COUNT-VARIABLE SRL-CONTROL)

FIND-CUSTOM-COL (FILENAME COL)

FIND-CUSTOM-COLS-FOR-FILENAME (FILENAME)

FIND-SSTRE2-STY (STY)

FIND-TUI-WORD (&REST ARGS)

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

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

FIND-UMAP-CUI (CUI)

FIND-UOBJ-MULTIWORD (STR OBJ-LOOKUP-FUN SORT-FUN KEY SRL ONLY-EXACT-IF-MATCH LIMIT &KEY EXTRA-LOOKUP-ARGS)

FIND-USMAP-CUI (CUI)

GEN-UCOLS

GEN-UFILES

GEN-UFILES-CUSTOM

INSERT-COL-VALUE (COL VALUE)

INSERT-USTATS (CONN NAME COUNT SRL)

INSERT-USTATS-COUNT (CONN NAME TABLE COUNT-VARIABLE SRL-CONTROL SRL)

LOOKUP-DB-NAME (DB)

LUI-LRL (LUI)

LUI-LRLUS (LUI)

MAKE-CUILUI (CUI LUI)

MAKE-CUISUI (CUI SUI)

MAKE-EMPTY-UCOL (COLNAME FILENAME)

MAKE-PREPARSE-HASH-TABLE

MAKE-UCOL (COL DES REF MIN AV MAX FIL DTY &KEY (SQLTYPE VARCHAR) (PARSE-FUN #'ADD-SQL-QUOTES) (QUOTE-STR ') (CUSTOM-VALUE-FUN))

MAKE-UCOL-FOR-COLUMN (COLNAME FILENAME UCOLS)

MAKE-UFILE (DIR FIL DES CLS RWS BTS FIELDS)

MAKE-USRL (CONN)

MAKE-USTATS (CONN)

MRCONSO-QUERY-WORD-CUI (WORD SAB SRL LIKE)

MRCONSO-QUERY-WORD-SUI (WORD SAB SRL LIKE)

MUTEX-SQL-EXECUTE (CMD)

MUTEX-SQL-QUERY (CMD &KEY (RESULT-TYPES AUTO))

NONENG-LANG-INDEX-FILES

PARSE-AUI (AUI)

PARSE-RUI (RUI)

QUERY-STRING-EVAL (TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) SINGLE DISTINCT ORDER LIKE LIMIT FILTER)

SAB-SRL (SAB)

SAB-SRLUS (SAB)

SET-UCOLS-FOR-UFILES (UFILES)

SOURCE-FILES (PATH)

SQL (STMT CONN)

SQL-CREATE-INDEXES-MYSQL (CONN INDEXES VERBOSE)

SQL-CREATE-SPECIAL-TABLES (CONN)

SQL-EXECUTE (CMD CONN)

SQL-QUERY (CMD CONN &KEY (RESULT-TYPES AUTO))

SUI-LRL (SUI)

SUI-LRLUS (SUI)

UMLS-CONNECTION-SPEC

UMLS-SQL (STMT)

MACRO

Public

Undocumented

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

Private

DEF-METACLASS-READER (FIELD)

Create function for reading slot of metaclass

DEF-METACLASS-READER-CAR (FIELD)

Create function for reading slot of metaclass

DEFINE-LOOKUP-DISPLAY (NEWFUNCNAME LOOKUP-FUNC)

Defines functions for looking up and displaying objects

UMLISP-QUERY (TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) SINGLE DISTINCT ORDER LIKE LIMIT FILTER (QUERY-CMD 'MUTEX-SQL-QUERY))

Query the UMLisp database. Return a list of umlisp objects whose name is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS

UMLISP-QUERY-EVAL (TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) SINGLE DISTINCT ORDER LIKE FILTER LIMIT)

Query the UMLisp database. Return a list of umlisp objects whose name is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS

WITH-BUFFERED-READING-UMLS-FILE ((LINE PATH) &BODY BODY)

Opens a UMLS and processes each parsed line with (body) argument

WITH-BUFFERED-UMLS-FILE ((LINE FILENAME) &BODY BODY)

Opens a UMLS and processes each parsed line with (body) argument

WITH-READING-UMLS-FILE ((LINE PATH) &BODY BODY)

Opens a UMLS and processes each parsed line with (body) argument

WITH-UMLS-FILE ((LINE UFILE) &BODY BODY)

Opens a UMLS and processes each parsed line with (body) argument

WITH-UMLS-UFILE ((LINE UFILE) &BODY BODY)

Opens a UMLS and processes each parsed line with (body) argument

Undocumented

COLLECT-UMLISP-QUERY ((TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) DISTINCT SINGLE ORDER LIKE (QUERY-CMD 'MUTEX-SQL-QUERY) FILTER LIMIT) &BODY BODY)

COLLECT-UMLISP-QUERY-EVAL ((TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) DISTINCT SINGLE ORDER LIKE FILTER LIMIT) &BODY BODY)

ENSURE-AUI-INTEGER (AUI)

ENSURE-CUI-INTEGER (CUI)

ENSURE-EUI-INTEGER (EUI)

ENSURE-LUI-INTEGER (LUI)

ENSURE-RUI-INTEGER (RUI)

ENSURE-SUI-INTEGER (SUI)

ENSURE-TUI-INTEGER (TUI)

QUERY-STRING (TABLE FIELDS SRL WHERE-NAME WHERE-VALUE &KEY (LRL KCUILRL) SINGLE DISTINCT ORDER LIKE LIMIT FILTER)

VFF (FILENAME FIELDNAME RECORD)

WITH-MUTEX-SQL ((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)

Private

Undocumented

FMT-RUI (RUI)

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)

Private

DTY (OBJECT)

new in 2002: suggested SQL datatype

SETFDTY (NEW-VALUE OBJECT)

new in 2002: suggested SQL datatype

Undocumented

ABR (OBJECT)

AGR (OBJECT)

ATNL (OBJECT)

AUI1 (OBJECT)

AUI2 (OBJECT)

AV (OBJECT)

SETFAV (NEW-VALUE OBJECT)

BTS (OBJECT)

SETFBTS (NEW-VALUE OBJECT)

CAS (OBJECT)

CENC (OBJECT)

CFR (OBJECT)

CIT (OBJECT)

CLS (OBJECT)

SETFCLS (NEW-VALUE OBJECT)

CMAX (OBJECT)

SETFCMAX (NEW-VALUE OBJECT)

CMIN (OBJECT)

SETFCMIN (NEW-VALUE OBJECT)

COL (OBJECT)

SETFCOL (NEW-VALUE OBJECT)

COM (OBJECT)

CUISUI (OBJECT)

CURVER (OBJECT)

CUSTOM-VALUE-FUN (OBJECT)

SETFCUSTOM-VALUE-FUN (NEW-VALUE OBJECT)

CXN (OBJECT)

CXTY (OBJECT)

DATATYPE (OBJECT)

SETFDATATYPE (NEW-VALUE OBJECT)

DES (OBJECT)

SETFDES (NEW-VALUE OBJECT)

DIR (OBJECT)

SETFDIR (NEW-VALUE OBJECT)

EUILIST (OBJECT)

EX (OBJECT)

FEA (OBJECT)

FIELDS (OBJECT)

SETFFIELDS (NEW-VALUE OBJECT)

FIL (OBJECT)

SETFFIL (NEW-VALUE OBJECT)

FMT (OBJECT)

SETFFMT (NEW-VALUE OBJECT)

FREQ (OBJECT)

SETFFREQ (NEW-VALUE OBJECT)

FROMEXPR (OBJECT)

FROMID (OBJECT)

FROMRES (OBJECT)

FROMRULE (OBJECT)

FROMSID (OBJECT)

FROMTYPE (OBJECT)

GEN (OBJECT)

GND (OBJECT)

HITS (OBJECT)

KCUILRL (OBJECT)

KCUILUI (OBJECT)

KCUISUI (OBJECT)

KLUILRL (OBJECT)

KSUILRL (OBJECT)

LS (OBJECT)

MAPATN (OBJECT)

MAPATV (OBJECT)

MAPRANK (OBJECT)

MAPRULE (OBJECT)

MAPSETCUI (OBJECT)

MAPSETSAB (OBJECT)

MAPSUBSETID (OBJECT)

MAPTYPE (OBJECT)

NAME (OBJECT)

NUM (OBJECT)

NWD (OBJECT)

PARSE-FUN (OBJECT)

SETFPARSE-FUN (NEW-VALUE OBJECT)

PAUI (OBJECT)

POS (OBJECT)

PSNMOD (OBJECT)

PTR (OBJECT)

QNT (OBJECT)

QUOTE-STR (OBJECT)

SETFQUOTE-STR (NEW-VALUE OBJECT)

REF (OBJECT)

SETFREF (NEW-VALUE OBJECT)

RG (OBJECT)

RH (OBJECT)

RIN (OBJECT)

RT (OBJECT)

RWS (OBJECT)

SETFRWS (NEW-VALUE OBJECT)

S#ABR (OBJECT)

S#AGR (OBJECT)

S#CMP (OBJECT)

S#HIER (OBJECT)

S#MAP (OBJECT)

S#MOD (OBJECT)

S#NOM (OBJECT)

S#PRN (OBJECT)

S#PRP (OBJECT)

S#SMAP (OBJECT)

S#SPL (OBJECT)

S#TRM (OBJECT)

S#TYP (OBJECT)

SABIN (OBJECT)

SCA (OBJECT)

SCA2 (OBJECT)

SF (OBJECT)

SON (OBJECT)

SPV (OBJECT)

SQLTYPE (OBJECT)

SETFSQLTYPE (NEW-VALUE OBJECT)

SRUI (OBJECT)

SSN (OBJECT)

STNRTN (OBJECT)

STYPE1 (OBJECT)

STYPE2 (OBJECT)

STYRL (OBJECT)

STYRL2 (OBJECT)

SUBDIR (OBJECT)

SETFSUBDIR (NEW-VALUE OBJECT)

SVER (OBJECT)

TABLE (OBJECT)

SETFTABLE (NEW-VALUE OBJECT)

TFR (OBJECT)

TOEXPR (OBJECT)

TOID (OBJECT)

TORES (OBJECT)

TORULE (OBJECT)

TOSID (OBJECT)

TOTYPE (OBJECT)

TTYL (OBJECT)

TYP (OBJECT)

UCOLS (OBJECT)

SETFUCOLS (NEW-VALUE OBJECT)

UXNW-CUILIST (OBJECT)

VEND (OBJECT)

VSTART (OBJECT)

WRD (OBJECT)

VARIABLE

Public

Undocumented

*CURRENT-SRL*

*UMLS-SQL-DB*

Private

*OCTET-SQL-STORAGE*

Used to deciding field lengths. Use nil if using UTF-8 database encoding. But, UTF-8 will cause MySQL to double the bytes used for fixed field sizes.

*UMLS-COLS*

List of meta column structures. Used when parsing text files.

*UMLS-FILES*

List of umls file structures. Used when parsing text files.

*UMLS-PATH*

Path for base of UMLS data files

+COL-DATATYPES+

SQL data types for each non-string column

+CUSTOM-COLS+

Custom columns to create.(filename, col, sqltype, value-func).

+CUSTOM-INDEX-COLS+

Indexes to custom tables

+CUSTOM-TABLES+

Custom tables to create

+INDEX-COLS+

Columns in files to index

Undocumented

*HAS-FIXNUM-CLASS*

*IS-LAT-TABLE-INIT*

*IS-REL-TABLE-INIT*

*LAT-INFO-TABLE*

*LEX-DIR*

*LEX-PATH*

*META-DIR*

*META-PATH*

*NET-DIR*

*NET-PATH*

*PREPARSE-HASH-INIT?*

*REL-INFO-TABLE*

*RELEASE*

*UMLS-SQL-HOST*

*UMLS-SQL-PASSWD*

*UMLS-SQL-TYPE*

*UMLS-SQL-USER*

*VFF-POSITION-HASH*

+DEFAULT-UMLS-DB+

+LANGUAGE-ABBREVIATIONS+

+RELATIONSHIP-ABBREVIATIONS+

+UMLS-SQL-MAP+

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

Private

UCOL

UMLS column

UCONSO

CONSO is a new concept from the RRF files.

UFILE

UMLS File

USTATS

Custom Table: UMLS Database statistics.

Undocumented

FREQ (OBJECT)

UHIER

UMAP

USMAP

UXW-NONENG

CONSTANT

Private

Undocumented

+CUISUI-SCALE+