org.apache.ctakes.drugner

Class DrugMention

java.lang.Object

org.apache.ctakes.drugner.DrugMention

All Implemented Interfaces:

DrugModel

public class DrugMention
extends java.lang.Object
implements DrugModel

Contains information from a single document - is not the result of data mining.

Field Summary

Fields

Modifier and Type	Field and Description
AssociatedPrimaryCodeElement	associatedCodePrimary
AssociatedPrimaryCodeElement	associatedCodeSecondary terminology unique identifier (e.g.
DrugChangeStatusElement	changeStatus aka change.
ConfidenceScoreElement	confidence
DosageElement	dosage e.g.
TextMentionElement	drugMentionText The word(s) in the note that indicate the drug.
DurationElement	duration e.g.
DateToken	endDate
boolean	findMaxValue
FormElement	form Span the drug form, if available.
FrequencyElement	frequency e.g.
FrequencyUnitElement	frequencyUnit e.g.
private double	holdLargestPeriod
private static java.util.regex.Pattern	lookForAlpha regex pattern to look for, in this case alpha upper and lower characters
private static java.util.regex.Pattern	lookForPercent regex pattern to look for, in this case alpha upper and lower characters
RouteElement	route e.g oral Topical Examples include medications applied onto the skin, asthma medications, enema, eye or ear drops, decongestants, vaginal creams.
StartDateElement	startDate If there is a specific date in the note associated with the drug mention, the specific date.
StrengthElement	strength
StrengthUnitElement	strengthUnit Span the drug form, if available.

Constructor Summary

Constructors

Constructor and Description
DrugMention(JCas jcas, int beginPos, int endPos)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	convertFromTextToNum(java.lang.String firstTerm)
java.lang.String	convertToChangeStatus(java.lang.String firstTerm)
private java.lang.String	findDosageElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findDrugChangeStatusElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findDurationElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findEndDateElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findFormElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findFrequencyElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findFrequencyUnitElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findRouteElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findStartDateElement(JCas jcas, int beginOffset, int endOffset)
private java.lang.String	findStrengthElement(JCas jcas, int beginOffset, int endOffset)
int	getChangeStatusBegin()
int	getChangeStatusEnd()
double	getConfidenceScoreElement()
int	getDosageBegin()
java.lang.String	getDosageElement()
int	getDosageEnd()
java.lang.String	getDrugChangeStatusElement()
int	getDuratationBegin()
int	getDuratationEnd()
java.lang.String	getDurationElement()
java.lang.String	getEndDateElement()
int	getFormBegin()
java.lang.String	getFormElement()
int	getFormEnd()
int	getFrequencyBegin()
java.lang.String	getFrequencyElement()
int	getFrequencyEnd()
java.lang.String	getFrequencyUnitElement()
int	getFUBegin()
int	getFUENd()
java.lang.String	getPrimaryAssociatedCodeElement()
int	getRouteBegin()
java.lang.String	getRouteElement()
int	getRouteEnd()
java.lang.String	getSecondaryAssociatedCodeElement()
java.lang.String	getStartDateElement()
int	getStrengthBegin()
java.lang.String	getStrengthElement()
int	getStrengthEnd()
int	getStrengthUnitBegin()
java.lang.String	getStrengthUnitElement()
int	getStrengthUnitEnd()
static int	indexOfRegex(java.lang.String lookIn, java.util.regex.Pattern lookFor) Scan a string for the first occurrence of some regex Pattern.
double	parseDoubleValue(java.lang.Object strength)
int	parseIntValue(java.lang.Object strength)
private java.lang.String	parseRegex(java.lang.String stringGlob)
void	setConfidenceScoreElement(double score, int beginOffset, int endOffset)
void	setDosageElement(java.lang.String dose, int beginOffset, int endOffset)
void	setDrugChangeStatusElement(java.lang.String name, int beginOffset, int endOffset)
void	setDurationElement(java.lang.String name, int beginOffset, int endOffset)
void	setEndDateElement(java.lang.String name, int beginOffset, int endOffset)
void	setFormElement(java.lang.String name, int beginOffset, int endOffset)
void	setFrequencyElement(java.lang.String name, int beginOffset, int endOffset)
void	setFrequencyUnitElement(java.lang.String name, int beginOffset, int endOffset)
void	setPrimaryAssociatedCodeElement(java.lang.String name, int beginOffset, int endOffset)
void	setRouteElement(java.lang.String name, int beginOffset, int endOffset)
void	setSecondaryAssociatedCodeElement(java.lang.String name, int beginOffset, int endOffset)
void	setStartDateElement(java.lang.String date, int beginOffset, int endOffset)
void	setStrengthElement(java.lang.String name, int beginOffset, int endOffset)
void	setStrengthUnitElement(java.lang.String name, int beginOffset, int endOffset)

Methods inherited from class java.lang.Object

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

Field Detail

drugMentionText

public TextMentionElement drugMentionText

The word(s) in the note that indicate the drug.

associatedCodePrimary

public AssociatedPrimaryCodeElement associatedCodePrimary

associatedCodeSecondary

public AssociatedPrimaryCodeElement associatedCodeSecondary

terminology unique identifier (e.g. RxNorm identifier). if not in the terminology, we will use the drug mention as the id.

startDate

public StartDateElement startDate

If there is a specific date in the note associated with the drug mention, the specific date. Also time might be capture by more general markers, e.g. "subsequently".

endDate

public DateToken endDate

dosage

public DosageElement dosage

e.g. 5 mg

frequency

public FrequencyElement frequency

e.g. twice daily

frequencyUnit

public FrequencyUnitElement frequencyUnit

e.g. twice daily

duration

public DurationElement duration

e.g. "for 2 weeks"

route

public RouteElement route

e.g oral Topical Examples include medications applied onto the skin, asthma medications, enema, eye or ear drops, decongestants, vaginal creams. Enteral (oral) Most drugs taken by mouth such as tablets or capsules. Enteral (gastric) Examples include medications given through a gastric or duodenal tube. Enteral (rectal) Drugs in suppositories or enema form. Parenteral (intravenous) Parenteral (intra-arterial) Parenteral (intramuscular) Parenteral (intracardiac) Parenteral (subcutaneous) Medications such as insulin. Parenteral (intrathecal) Into the spinal canal. Parenteral (intraperitoneal) Parenteral (transdermal) Such as patches. Parenteral (transmucosal)

strength

public StrengthElement strength

strengthUnit

public StrengthUnitElement strengthUnit

Span the drug form, if available. The spanned mention needs to be mapped to the standard form available in the dropdown menu. In general don't infer. However, for a medication described in terms of cc or mL, the number of cc's or mL's is usually not a strength - for example "5 cc 0.5%" (or 5 mL 0.5%), indicates a strength of 0.5% -- for those, create a Form, with "cc" or "mL" spanned, and mapped to liquid, so that we capture the unit such as cc or mL.

form

public FormElement form

Span the drug form, if available. The spanned mention needs to be mapped to the standard form available in the dropdown menu. In general don't infer. However, for a medication described in terms of cc or mL, the number of cc's or mL's is usually not a strength - for example "5 cc 0.5%" (or 5 mL 0.5%), indicates a strength of 0.5% -- for those, create a Form, with "cc" or "mL" spanned, and mapped to liquid, so that we capture the unit such as cc or mL.

changeStatus

public DrugChangeStatusElement changeStatus

aka change. - start: refers to an explicit mention of when the drug was started - stop: refers to an explicit mention of when the drug was stopped - increase and decrease: refer to explicit mentions of drug attribute changes - noChange: nothing is explicitly stated regarding changes. This will be the default case and does not need to be created. If there is some mention on the text such as "I told the patient to continue with his dosage of XXX 300 mg", then there would be textual evidence for noChange.

confidence

public ConfidenceScoreElement confidence

findMaxValue

public boolean findMaxValue

lookForAlpha

private static final java.util.regex.Pattern lookForAlpha

regex pattern to look for, in this case alpha upper and lower characters

lookForPercent

private static final java.util.regex.Pattern lookForPercent

regex pattern to look for, in this case alpha upper and lower characters

holdLargestPeriod

private double holdLargestPeriod

Constructor Detail

DrugMention

public DrugMention(JCas jcas,
           int beginPos,
           int endPos)

Method Detail

setPrimaryAssociatedCodeElement

public void setPrimaryAssociatedCodeElement(java.lang.String name,
                                   int beginOffset,
                                   int endOffset)

Specified by:

setPrimaryAssociatedCodeElement in interface DrugModel

setSecondaryAssociatedCodeElement

public void setSecondaryAssociatedCodeElement(java.lang.String name,
                                     int beginOffset,
                                     int endOffset)

Specified by:

setSecondaryAssociatedCodeElement in interface DrugModel

setStartDateElement

public void setStartDateElement(java.lang.String date,
                       int beginOffset,
                       int endOffset)

Specified by:

setStartDateElement in interface DrugModel

setEndDateElement

public void setEndDateElement(java.lang.String name,
                     int beginOffset,
                     int endOffset)

Specified by:

setEndDateElement in interface DrugModel

setDosageElement

public void setDosageElement(java.lang.String dose,
                    int beginOffset,
                    int endOffset)

Specified by:

setDosageElement in interface DrugModel

setFrequencyElement

public void setFrequencyElement(java.lang.String name,
                       int beginOffset,
                       int endOffset)

Specified by:

setFrequencyElement in interface DrugModel

setFrequencyUnitElement

public void setFrequencyUnitElement(java.lang.String name,
                           int beginOffset,
                           int endOffset)

Specified by:

setFrequencyUnitElement in interface DrugModel

setFormElement

public void setFormElement(java.lang.String name,
                  int beginOffset,
                  int endOffset)

Specified by:

setFormElement in interface DrugModel

setDurationElement

public void setDurationElement(java.lang.String name,
                      int beginOffset,
                      int endOffset)

Specified by:

setDurationElement in interface DrugModel

setRouteElement

public void setRouteElement(java.lang.String name,
                   int beginOffset,
                   int endOffset)

Specified by:

setRouteElement in interface DrugModel

setDrugChangeStatusElement

public void setDrugChangeStatusElement(java.lang.String name,
                              int beginOffset,
                              int endOffset)

Specified by:

setDrugChangeStatusElement in interface DrugModel

setConfidenceScoreElement

public void setConfidenceScoreElement(double score,
                             int beginOffset,
                             int endOffset)

Specified by:

setConfidenceScoreElement in interface DrugModel

setStrengthElement

public void setStrengthElement(java.lang.String name,
                      int beginOffset,
                      int endOffset)

Specified by:

setStrengthElement in interface DrugModel

getStrengthUnitElement

public java.lang.String getStrengthUnitElement()

Specified by:

getStrengthUnitElement in interface DrugModel

setStrengthUnitElement

public void setStrengthUnitElement(java.lang.String name,
                          int beginOffset,
                          int endOffset)

Specified by:

setStrengthUnitElement in interface DrugModel

getPrimaryAssociatedCodeElement

public java.lang.String getPrimaryAssociatedCodeElement()

Specified by:

getPrimaryAssociatedCodeElement in interface DrugModel

getSecondaryAssociatedCodeElement

public java.lang.String getSecondaryAssociatedCodeElement()

Specified by:

getSecondaryAssociatedCodeElement in interface DrugModel

getStartDateElement

public java.lang.String getStartDateElement()

Specified by:

getStartDateElement in interface DrugModel

getEndDateElement

public java.lang.String getEndDateElement()

Specified by:

getEndDateElement in interface DrugModel

getDosageElement

public java.lang.String getDosageElement()

Specified by:

getDosageElement in interface DrugModel

getFrequencyElement

public java.lang.String getFrequencyElement()

Specified by:

getFrequencyElement in interface DrugModel

getFrequencyUnitElement

public java.lang.String getFrequencyUnitElement()

Specified by:

getFrequencyUnitElement in interface DrugModel

getFormElement

public java.lang.String getFormElement()

Specified by:

getFormElement in interface DrugModel

getDurationElement

public java.lang.String getDurationElement()

Specified by:

getDurationElement in interface DrugModel

getRouteElement

public java.lang.String getRouteElement()

Specified by:

getRouteElement in interface DrugModel

getDrugChangeStatusElement

public java.lang.String getDrugChangeStatusElement()

Specified by:

getDrugChangeStatusElement in interface DrugModel

getStrengthElement

public java.lang.String getStrengthElement()

Specified by:

getStrengthElement in interface DrugModel

getConfidenceScoreElement

public double getConfidenceScoreElement()

Specified by:

getConfidenceScoreElement in interface DrugModel

findStartDateElement

private java.lang.String findStartDateElement(JCas jcas,
                                    int beginOffset,
                                    int endOffset)

findEndDateElement

private java.lang.String findEndDateElement(JCas jcas,
                                  int beginOffset,
                                  int endOffset)

findDosageElement

private java.lang.String findDosageElement(JCas jcas,
                                 int beginOffset,
                                 int endOffset)

findFormElement

private java.lang.String findFormElement(JCas jcas,
                               int beginOffset,
                               int endOffset)

findFrequencyElement

private java.lang.String findFrequencyElement(JCas jcas,
                                    int beginOffset,
                                    int endOffset)

findFrequencyUnitElement

private java.lang.String findFrequencyUnitElement(JCas jcas,
                                        int beginOffset,
                                        int endOffset)

findDurationElement

private java.lang.String findDurationElement(JCas jcas,
                                   int beginOffset,
                                   int endOffset)

findRouteElement

private java.lang.String findRouteElement(JCas jcas,
                                int beginOffset,
                                int endOffset)

findDrugChangeStatusElement

private java.lang.String findDrugChangeStatusElement(JCas jcas,
                                           int beginOffset,
                                           int endOffset)

findStrengthElement

private java.lang.String findStrengthElement(JCas jcas,
                                   int beginOffset,
                                   int endOffset)

parseRegex

private java.lang.String parseRegex(java.lang.String stringGlob)

parseIntValue

public int parseIntValue(java.lang.Object strength)

parseDoubleValue

public double parseDoubleValue(java.lang.Object strength)

convertFromTextToNum

public java.lang.String convertFromTextToNum(java.lang.String firstTerm)

convertToChangeStatus

public java.lang.String convertToChangeStatus(java.lang.String firstTerm)

getDosageBegin

public int getDosageBegin()

getDosageEnd

public int getDosageEnd()

getFrequencyBegin

public int getFrequencyBegin()

getFrequencyEnd

public int getFrequencyEnd()

getFUBegin

public int getFUBegin()

getFUENd

public int getFUENd()

getFormBegin

public int getFormBegin()

getFormEnd

public int getFormEnd()

getDuratationBegin

public int getDuratationBegin()

getDuratationEnd

public int getDuratationEnd()

getRouteBegin

public int getRouteBegin()

getRouteEnd

public int getRouteEnd()

getStrengthUnitBegin

public int getStrengthUnitBegin()

getStrengthUnitEnd

public int getStrengthUnitEnd()

getStrengthBegin

public int getStrengthBegin()

getStrengthEnd

public int getStrengthEnd()

getChangeStatusBegin

public int getChangeStatusBegin()

getChangeStatusEnd

public int getChangeStatusEnd()

indexOfRegex

public static int indexOfRegex(java.lang.String lookIn,
               java.util.regex.Pattern lookFor)

Scan a string for the first occurrence of some regex Pattern.

Parameters:

lookForAlpha - the pattern to look for

lookIn - the String to scan.

Returns:

offset relative to start of lookIn where it first found the pattern, -1 if not found.