ch.epfl.bbp.uima.utils

Class ExtractAbbrev

java.lang.Object

ch.epfl.bbp.uima.utils.ExtractAbbrev

public class ExtractAbbrev
extends 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. Software available here: http://biotext.berkeley.edu/code/abbrev/ExtractAbbrev.java This version has been modified to allow String input. 08/19/08

Constructor Summary

Constructors

Constructor and Description
ExtractAbbrev()

Method Summary

Methods

Modifier and Type	Method and Description
List<String>	extractAbbrPair(String shortForm, String longForm)
Map<String,String>	extractAbbrPairs(String inFile) Method altered, 08/19/08.
Map<String,String>	extractAbbrPairs(String inputText, boolean isFileName) Extract abbreviation pairs directly from input text.
String	findBestLongForm(String shortForm, String longForm)
boolean	hasCapital(String str)
boolean	hasLetter(String str)
boolean	isTrueDefinition(String shortForm, String longForm)
boolean	isValidShortForm(String str)
void	loadTrueDefinitions(String inFile)
static void	main(String[] args)
static void	usage()

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractAbbrev

public ExtractAbbrev()

Method Detail

isValidShortForm

public boolean isValidShortForm(String str)

hasLetter

public boolean hasLetter(String str)

hasCapital

public boolean hasCapital(String str)

loadTrueDefinitions

public void loadTrueDefinitions(String inFile)

isTrueDefinition

public boolean isTrueDefinition(String shortForm,
                       String longForm)

extractAbbrPairs

public Map<String,String> extractAbbrPairs(String inFile)

Method altered, 08/19/08. Processing code moved to extractAbbrPairs(Reader) to facilitate extraction of abbreviations directly from text (i.e. a String not a file).

Parameters:

inFile -

Returns:

extractAbbrPairs

public Map<String,String> extractAbbrPairs(String inputText,
                                  boolean isFileName)

Extract abbreviation pairs directly from input text. Method added by University of Colorado, Center for Computational Pharmacology, 08/19/08

Parameters:

inputText -

Returns:

findBestLongForm

public String findBestLongForm(String shortForm,
                      String longForm)

extractAbbrPair

public List<String> extractAbbrPair(String shortForm,
                           String longForm)

usage

public static void usage()

main

public static void main(String[] args)