martin.common
Class ExtractAbbrev

java.lang.Object
  martin.common.ExtractAbbrev

public class ExtractAbbrev
extends java.lang.Object

The ExtractAbbrev class implements a simple algorithm for extraction of abbreviations and their definitions from biomedical text. Abbreviations (short forms) are extracted from the input file, and those abbreviations for which a definition (long form) is found are printed out, along with that definition, one per line. A file consisting of short-form/long-form pairs (tab separated) can be specified in tandem with the -testlist option for the purposes of evaluating the algorithm.

Version:

03/12/03

Author:

Ariel Schwartz

See Also:

A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text A.S. Schwartz, M.A. Hearst; Pacific Symposium on Biocomputing 8:451-462(2003) for a detailed description of the algorithm. http://biotext.berkeley.edu/software.html

Field Summary

(package private) char	delimiter
(package private) int	falseNegatives
(package private) int	falsePositives
(package private) java.util.HashMap	mStats
(package private) java.util.HashMap	mTestDefinitions
(package private) boolean	testMode
(package private) int	trueNegatives
(package private) int	truePositives

Constructor Summary

ExtractAbbrev()

Method Summary

private Pair<java.lang.String>	extractAbbrPair(java.lang.String shortForm, java.lang.String longForm)
java.util.Map<java.lang.String,java.lang.String>	extractAbbrPairs(java.io.File inFile)
private java.lang.String	findBestLongForm(java.lang.String shortForm, java.lang.String longForm)
private boolean	hasCapital(java.lang.String str)
private boolean	hasLetter(java.lang.String str)
private boolean	isTrueDefinition(java.lang.String shortForm, java.lang.String longForm)
private boolean	isValidShortForm(java.lang.String str)
private void	loadTrueDefinitions(java.lang.String inFile)
static void	main(java.lang.String[] args)
private static void	usage()

Methods inherited from class java.lang.Object

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

Field Detail

mTestDefinitions

java.util.HashMap mTestDefinitions

mStats

java.util.HashMap mStats

truePositives

int truePositives

falsePositives

int falsePositives

falseNegatives

int falseNegatives

trueNegatives

int trueNegatives

delimiter

char delimiter

testMode

boolean testMode

Constructor Detail

ExtractAbbrev

public ExtractAbbrev()

Method Detail

isValidShortForm

private boolean isValidShortForm(java.lang.String str)

hasLetter

private boolean hasLetter(java.lang.String str)

hasCapital

private boolean hasCapital(java.lang.String str)

loadTrueDefinitions

private void loadTrueDefinitions(java.lang.String inFile)

isTrueDefinition

private boolean isTrueDefinition(java.lang.String shortForm,
                                 java.lang.String longForm)

extractAbbrPairs

public java.util.Map<java.lang.String,java.lang.String> extractAbbrPairs(java.io.File inFile)

findBestLongForm

private java.lang.String findBestLongForm(java.lang.String shortForm,
                                          java.lang.String longForm)

extractAbbrPair

private Pair<java.lang.String> extractAbbrPair(java.lang.String shortForm,
                                               java.lang.String longForm)

usage

private static void usage()

main

public static void main(java.lang.String[] args)