Package org.ohnlp.ae.medxn

Class MedExtAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.ohnlp.ae.medxn.MedExtAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class MedExtAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Associate medication with attributes.

Author:

Sunghwan Sohn

Field Summary

Fields

Modifier and Type	Field	Description
static int	SENT_WINDOW_SPAN
static int	SENT_WINDOW_SPAN_DUR

Constructor Summary

Constructors

Constructor	Description
MedExtAnnotator()

Method Summary

Modifier and Type	Method	Description
protected int	contains(int b1, int e1, int b2, int e2)	Returns 1 if 1 contains or equal to 2 Returns 2 if 2 contains or equal to 1 Returns 0 otherwise
void	initialize(org.apache.uima.UimaContext uimaContext)
protected boolean	isFalseMed1(String med)	Check if the given drug is true or not
void	process(org.apache.uima.jcas.JCas jcas)
protected int[]	setWindow(org.apache.uima.jcas.JCas jcas, de.julielab.jcore.types.medical.Medication drug, int nextDrugBegin, int prevDrugEnd, int windowSpan)	NOTE THAT THIS IS SPECIFIC FOR MAYO DATA return the offsets: begin of the given drug and the smaller of 1) the end of +2 sentences or 2) begin of the next drug Mayo specific: "BUT if there is newline and it does not start with Instruction or Indication, the end becomes newline"

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Field Detail

SENT_WINDOW_SPAN

public static final int SENT_WINDOW_SPAN

See Also:

Constant Field Values

SENT_WINDOW_SPAN_DUR

public static final int SENT_WINDOW_SPAN_DUR

See Also:

Constant Field Values

Constructor Detail

MedExtAnnotator

public MedExtAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext uimaContext)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas jcas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

setWindow

protected int[] setWindow(org.apache.uima.jcas.JCas jcas,
                          de.julielab.jcore.types.medical.Medication drug,
                          int nextDrugBegin,
                          int prevDrugEnd,
                          int windowSpan)

NOTE THAT THIS IS SPECIFIC FOR MAYO DATA return the offsets: begin of the given drug and the smaller of 1) the end of +2 sentences or 2) begin of the next drug Mayo specific: "BUT if there is newline and it does not start with Instruction or Indication, the end becomes newline"

Parameters:

jcas -

drug -

nextDrugBegin -

Returns:

isFalseMed1

protected boolean isFalseMed1(String med)

Check if the given drug is true or not

Parameters:

md -

Returns:

true if potentially false medication

contains

protected int contains(int b1,
                       int e1,
                       int b2,
                       int e2)

Returns 1 if 1 contains or equal to 2 Returns 2 if 2 contains or equal to 1 Returns 0 otherwise