gov.nih.nlm.nls.stmt.Synonym

Class SynonymsTable

java.lang.Object

gov.nih.nlm.nls.stmt.Synonym.SynonymsTable

public class SynonymsTable
extends java.lang.Object

This program is used to load synonyms to synonoym table from files including normalization. The following three steps are used:

• read in synonyms from file(s)
• load to a Hashtable<String, HashSet<String>>
• sent to an outputs file

This class is capable of handling following formats:

• use # for comments convert to multiple synonym pairs
• duplicated synonym pairs, remove
• redundancy (synonym1 = synonym2), remove
• norm redundancy (identical normTerm) as synonym, remove
• non-symmetric synonyms, automatically generate bi-directional synonyms
• mulitple synonym pairs in one line: synonym1|synonym2|synonym3|...,

• Program normalize key by SynonymNorm: -f:g:rs:Ct:o:l

This file should be run at pre-process to improve performance Notes: This class is diferent from CuiMap as follows:

• SynonymNorm is different: => -f:g:rs:Ct:o:l vs. f:g:rs:o:l:Ct => no empty string return (return original inStr instead)
• remove synonym 1 = synonym 2
• provide options for not checking LvgNorm form on the synonym 1 and 2

History:

Version:

V-2014

Author:

NLM NLS Development Team

Method Summary

Methods

Modifier and Type	Method and Description
static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>>	AddSynonymsFromFile(java.lang.String inFile, gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi) Get the the key-values table of norm-synonym 1|synonym 2 by loading from a file.
static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>>	AddSynonymsFromFile(java.lang.String inFile, gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi, gov.nih.nlm.nls.lvg.Api.NormApi normApi) Get the the key-values table of norm-synonym 1|synonym 2 by loading from a file.
static void	AppendSynonymsFromFile(java.lang.String inFile, gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable) Add norm-synonym 1|synonym 2 from a file to the the key-values table.
static void	AppendSynonymsFromFile(java.lang.String inFile, gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi, gov.nih.nlm.nls.lvg.Api.NormApi normApi, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable) Add norm-synonym 1|synonym 2 from a file to the the key-values table.
static void	PrintTableToFile(java.lang.String outFile, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable) Send the key-values table of norm-synonym 1|synonym 2 to a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

AddSynonymsFromFile

public static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> AddSynonymsFromFile(java.lang.String inFile,
                                                                                            gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi)

Get the the key-values table of norm-synonym 1|synonym 2 by loading from a file.

Parameters:

inFile - the file includes norm-synonym 1|synonym 2 to be loaded

lvgApi - LvgApi object from Lexical Tools

Returns:

the key-values table of norm-synonym 1|synonym 2

AddSynonymsFromFile

public static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> AddSynonymsFromFile(java.lang.String inFile,
                                                                                            gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi,
                                                                                            gov.nih.nlm.nls.lvg.Api.NormApi normApi)

Get the the key-values table of norm-synonym 1|synonym 2 by loading from a file. This method eliminates synonyms has same lvgNorm form because it is used in UMLS-CORE and same lvgNorm form leads to same CUI mapping.

Parameters:

inFile - the file includes norm-synonym 1|synonym 2 to be loaded

lvgApi - LvgApi object from Lexical Tools

normApi - NormApi object from Lexical Tools

Returns:

the key-values table of norm-synonym 1|synonym 2

AppendSynonymsFromFile

public static void AppendSynonymsFromFile(java.lang.String inFile,
                          gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi,
                          java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable)

Add norm-synonym 1|synonym 2 from a file to the the key-values table.

Parameters:

inFile - the file includes norm-synonym 1|synonym 2 to be loaded

lvgApi - LvgApi object from Lexical Tools

synonymsTable - the key-values table of norm-synonym 1|synonym 2

AppendSynonymsFromFile

public static void AppendSynonymsFromFile(java.lang.String inFile,
                          gov.nih.nlm.nls.lvg.Api.LvgApi lvgApi,
                          gov.nih.nlm.nls.lvg.Api.NormApi normApi,
                          java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable)

Add norm-synonym 1|synonym 2 from a file to the the key-values table. This method eliminates synonyms has same lvgNorm form because it is used in UMLS-CORE and same lvgNorm form leads to same CUI mapping.

Parameters:

inFile - the file includes norm-synonym 1|synonym 2 to be loaded

lvgApi - LvgApi object from Lexical Tools

normApi - NormApi object from Lexical Tools

synonymsTable - the key-values table of norm-synonym 1|synonym 2

PrintTableToFile

public static void PrintTableToFile(java.lang.String outFile,
                    java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> synonymsTable)

Send the key-values table of norm-synonym 1|synonym 2 to a file.

Parameters:

outFile - the output file for norm-synonym 1|synonym 2

synonymsTable - the key-values table of norm-synonym 1|synonym 2