dragon.nlp.ontology.umls

Class UmlsExactOntology

java.lang.Object

dragon.nlp.ontology.AbstractOntology

dragon.nlp.ontology.umls.UmlsOntology

dragon.nlp.ontology.umls.UmlsExactOntology

All Implemented Interfaces:

Ontology

Direct Known Subclasses:

UmlsDBOntology, UmlsFileBackedOntology

public abstract class UmlsExactOntology
extends UmlsOntology

UMLS ontology for extracting UMLS defined medical concepts (CUIs) from text

Description:

Copyright: Copyright (c) 2005

Company: IST, Drexel University

Version:

1.0

Author:

Davis Zhou

Constructor Summary

Constructors

Constructor and Description
UmlsExactOntology(Lemmatiser lemmatiser)

Method Summary

Modifier and Type	Method and Description
String	buildNormalizedTerm(Word start, Word end)
ArrayList	findAllTerms(Word start) Finds out all terms beginning with the given word
ArrayList	findAllTerms(Word start, Word end) Finds out all terms between the starting word and the ending word.
Term	findTerm(Word start) Finds the longest term starting with the given word.
Term	findTerm(Word start, Word end) Finds the longest term starting with given word and ending no later than the given word.
abstract String[]	getCUI(String term) Gets all possible concept ids the specified term has
String[]	getCUI(Word starting, Word ending) Gets all possible concept ids the specified term has
abstract String[]	getSemanticType(String cui) Gets all possible semantic types of the given concept
String[]	getSemanticType(String[] cuis) Gets all possible semantic types of the given concepts
abstract boolean	isTerm(String term) Tests if the given term is defined in the ontology.
boolean	isTerm(Word starting, Word ending) Tests if the term specified by the starting word and the ending word is a term in the ontology.

Methods inherited from class dragon.nlp.ontology.AbstractOntology

buildString, getAdjectiveTermOption, getCoordinateOption, getLemma, getLemmaOption, getNonBoundaryPunctuation, getNPPOption, getSemanticNet, getSenseDisambiguationOption, getSimilarityMetric, isBoundaryWord, isStartingWord, isUsefulForTerm, setAdjectiveTermOption, setCoordinateOption, setLemmaOption, setNonBoundaryPunctuation, setNPPOption, setSenseDisambiguationOption

Methods inherited from class java.lang.Object

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

Constructor Detail

UmlsExactOntology

public UmlsExactOntology(Lemmatiser lemmatiser)

Method Detail

getSemanticType

public String[] getSemanticType(String[] cuis)

Description copied from interface: Ontology

Gets all possible semantic types of the given concepts

Parameters:

cuis - the set of concepts

Returns:

all possible semantic types of the given concepts

getSemanticType

public abstract String[] getSemanticType(String cui)

Description copied from interface: Ontology

Gets all possible semantic types of the given concept

Parameters:

cui - the concept id

Returns:

all possible semantic types of the given concept.

getCUI

public abstract String[] getCUI(String term)

Description copied from interface: Ontology

Gets all possible concept ids the specified term has

Parameters:

term - the term for testing

Returns:

all possible concept ids if the specified term exists in the ontology, otherwise null

getCUI

public String[] getCUI(Word starting,
                       Word ending)

Description copied from interface: Ontology

Gets all possible concept ids the specified term has

Parameters:

starting - the starting word of the term.

ending - the ending word of the term.

Returns:

all possible concept ids if the specified term exists in the ontology, otherwise null

isTerm

public abstract boolean isTerm(String term)

Description copied from interface: Ontology

Tests if the given term is defined in the ontology.

Parameters:

term - the term for testing

Returns:

true if the given term is defined in the ontology.

isTerm

public boolean isTerm(Word starting,
                      Word ending)

Description copied from interface: Ontology

Tests if the term specified by the starting word and the ending word is a term in the ontology.

Parameters:

starting - the starting word of the term.

ending - the ending word of the term.

Returns:

true if the term is defined in the ontology.

findAllTerms

public ArrayList findAllTerms(Word start)

Description copied from interface: Ontology

Finds out all terms beginning with the given word

Parameters:

start - the starting word

Returns:

a list of terms

findAllTerms

public ArrayList findAllTerms(Word start,
                              Word end)

Description copied from interface: Ontology

Finds out all terms between the starting word and the ending word.

Parameters:

start - the starting word

end - the ending word

Returns:

a list of terms

findTerm

public Term findTerm(Word start)

Description copied from interface: Ontology

Finds the longest term starting with the given word.

Parameters:

start - the starting word

Returns:

the term if exists, otherwise null

findTerm

public Term findTerm(Word start,
                     Word end)

Description copied from interface: Ontology

Finds the longest term starting with given word and ending no later than the given word.

Parameters:

start - the starting word

end - the ending word

Returns:

the term if exists, otherwise null

buildNormalizedTerm

public String buildNormalizedTerm(Word start,
                                  Word end)