DrugMention (Apache cTAKES 4.0.0 API)

java.lang.Object
- org.apache.ctakes.drugner.DrugMention

All Implemented Interfaces:

DrugModel
```
public class DrugMention
extends 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.
`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(org.apache.uima.jcas.JCas jcas, int beginPos, int endPos)

Constructors
Constructor and Description
`DrugMention(org.apache.uima.jcas.JCas jcas, int beginPos, int endPos)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`convertFromTextToNum(String firstTerm)`
`String`	`convertToChangeStatus(String firstTerm)`
`int`	`getChangeStatusBegin()`
`int`	`getChangeStatusEnd()`
`double`	`getConfidenceScoreElement()`
`int`	`getDosageBegin()`
`String`	`getDosageElement()`
`int`	`getDosageEnd()`
`String`	`getDrugChangeStatusElement()`
`int`	`getDuratationBegin()`
`int`	`getDuratationEnd()`
`String`	`getDurationElement()`
`String`	`getEndDateElement()`
`int`	`getFormBegin()`
`String`	`getFormElement()`
`int`	`getFormEnd()`
`int`	`getFrequencyBegin()`
`String`	`getFrequencyElement()`
`int`	`getFrequencyEnd()`
`String`	`getFrequencyUnitElement()`
`int`	`getFUBegin()`
`int`	`getFUENd()`
`String`	`getPrimaryAssociatedCodeElement()`
`int`	`getRouteBegin()`
`String`	`getRouteElement()`
`int`	`getRouteEnd()`
`String`	`getSecondaryAssociatedCodeElement()`
`String`	`getStartDateElement()`
`int`	`getStrengthBegin()`
`String`	`getStrengthElement()`
`int`	`getStrengthEnd()`
`int`	`getStrengthUnitBegin()`
`String`	`getStrengthUnitElement()`
`int`	`getStrengthUnitEnd()`
`static int`	`indexOfRegex(String lookIn, Pattern lookFor)` Scan a string for the first occurrence of some regex Pattern.
`double`	`parseDoubleValue(Object strength)`
`int`	`parseIntValue(Object strength)`
`void`	`setConfidenceScoreElement(double score, int beginOffset, int endOffset)`
`void`	`setDosageElement(String dose, int beginOffset, int endOffset)`
`void`	`setDrugChangeStatusElement(String name, int beginOffset, int endOffset)`
`void`	`setDurationElement(String name, int beginOffset, int endOffset)`
`void`	`setEndDateElement(String name, int beginOffset, int endOffset)`
`void`	`setFormElement(String name, int beginOffset, int endOffset)`
`void`	`setFrequencyElement(String name, int beginOffset, int endOffset)`
`void`	`setFrequencyUnitElement(String name, int beginOffset, int endOffset)`
`void`	`setPrimaryAssociatedCodeElement(String name, int beginOffset, int endOffset)`
`void`	`setRouteElement(String name, int beginOffset, int endOffset)`
`void`	`setSecondaryAssociatedCodeElement(String name, int beginOffset, int endOffset)`
`void`	`setStartDateElement(String date, int beginOffset, int endOffset)`
`void`	`setStrengthElement(String name, int beginOffset, int endOffset)`
`void`	`setStrengthUnitElement(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
```
- Constructor Detail
  - DrugMention
```
public DrugMention(org.apache.uima.jcas.JCas jcas,
                   int beginPos,
                   int endPos)
```
- Method Detail
  - setPrimaryAssociatedCodeElement
```
public void setPrimaryAssociatedCodeElement(String name,
                                            int beginOffset,
                                            int endOffset)
```
    Specified by:
    
    setPrimaryAssociatedCodeElement in interface DrugModel
  - setSecondaryAssociatedCodeElement
```
public void setSecondaryAssociatedCodeElement(String name,
                                              int beginOffset,
                                              int endOffset)
```
    Specified by:
    
    setSecondaryAssociatedCodeElement in interface DrugModel
  - setStartDateElement
```
public void setStartDateElement(String date,
                                int beginOffset,
                                int endOffset)
```
    Specified by:
    
    setStartDateElement in interface DrugModel
  - setEndDateElement
```
public void setEndDateElement(String name,
                              int beginOffset,
                              int endOffset)
```
    Specified by:
    
    setEndDateElement in interface DrugModel
  - setDosageElement
```
public void setDosageElement(String dose,
                             int beginOffset,
                             int endOffset)
```
    Specified by:
    
    setDosageElement in interface DrugModel
  - setFrequencyElement
```
public void setFrequencyElement(String name,
                                int beginOffset,
                                int endOffset)
```
    Specified by:
    
    setFrequencyElement in interface DrugModel
  - setFrequencyUnitElement
```
public void setFrequencyUnitElement(String name,
                                    int beginOffset,
                                    int endOffset)
```
    Specified by:
    
    setFrequencyUnitElement in interface DrugModel
  - setFormElement
```
public void setFormElement(String name,
                           int beginOffset,
                           int endOffset)
```
    Specified by:
    
    setFormElement in interface DrugModel
  - setDurationElement
```
public void setDurationElement(String name,
                               int beginOffset,
                               int endOffset)
```
    Specified by:
    
    setDurationElement in interface DrugModel
  - setRouteElement
```
public void setRouteElement(String name,
                            int beginOffset,
                            int endOffset)
```
    Specified by:
    
    setRouteElement in interface DrugModel
  - setDrugChangeStatusElement
```
public void setDrugChangeStatusElement(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(String name,
                               int beginOffset,
                               int endOffset)
```
    Specified by:
    
    setStrengthElement in interface DrugModel
  - getStrengthUnitElement
```
public String getStrengthUnitElement()
```
    Specified by:
    
    getStrengthUnitElement in interface DrugModel
  - setStrengthUnitElement
```
public void setStrengthUnitElement(String name,
                                   int beginOffset,
                                   int endOffset)
```
    Specified by:
    
    setStrengthUnitElement in interface DrugModel
  - getPrimaryAssociatedCodeElement
```
public String getPrimaryAssociatedCodeElement()
```
    Specified by:
    
    getPrimaryAssociatedCodeElement in interface DrugModel
  - getSecondaryAssociatedCodeElement
```
public String getSecondaryAssociatedCodeElement()
```
    Specified by:
    
    getSecondaryAssociatedCodeElement in interface DrugModel
  - getStartDateElement
```
public String getStartDateElement()
```
    Specified by:
    
    getStartDateElement in interface DrugModel
  - getEndDateElement
```
public String getEndDateElement()
```
    Specified by:
    
    getEndDateElement in interface DrugModel
  - getDosageElement
```
public String getDosageElement()
```
    Specified by:
    
    getDosageElement in interface DrugModel
  - getFrequencyElement
```
public String getFrequencyElement()
```
    Specified by:
    
    getFrequencyElement in interface DrugModel
  - getFrequencyUnitElement
```
public String getFrequencyUnitElement()
```
    Specified by:
    
    getFrequencyUnitElement in interface DrugModel
  - getFormElement
```
public String getFormElement()
```
    Specified by:
    
    getFormElement in interface DrugModel
  - getDurationElement
```
public String getDurationElement()
```
    Specified by:
    
    getDurationElement in interface DrugModel
  - getRouteElement
```
public String getRouteElement()
```
    Specified by:
    
    getRouteElement in interface DrugModel
  - getDrugChangeStatusElement
```
public String getDrugChangeStatusElement()
```
    Specified by:
    
    getDrugChangeStatusElement in interface DrugModel
  - getStrengthElement
```
public String getStrengthElement()
```
    Specified by:
    
    getStrengthElement in interface DrugModel
  - getConfidenceScoreElement
```
public double getConfidenceScoreElement()
```
    Specified by:
    
    getConfidenceScoreElement in interface DrugModel
  - parseIntValue
```
public int parseIntValue(Object strength)
```
  - parseDoubleValue
```
public double parseDoubleValue(Object strength)
```
  - convertFromTextToNum
```
public String convertFromTextToNum(String firstTerm)
```
  - convertToChangeStatus
```
public String convertToChangeStatus(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(String lookIn,
                               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.

Class DrugMention

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

drugMentionText

associatedCodePrimary

associatedCodeSecondary

startDate

endDate

dosage

frequency

frequencyUnit

duration

route

strength

strengthUnit

form

changeStatus

confidence

findMaxValue

Constructor Detail

DrugMention

Method Detail

setPrimaryAssociatedCodeElement

setSecondaryAssociatedCodeElement

setStartDateElement

setEndDateElement

setDosageElement

setFrequencyElement

setFrequencyUnitElement

setFormElement

setDurationElement

setRouteElement

setDrugChangeStatusElement

setConfidenceScoreElement

setStrengthElement

getStrengthUnitElement

setStrengthUnitElement

getPrimaryAssociatedCodeElement

getSecondaryAssociatedCodeElement

getStartDateElement

getEndDateElement

getDosageElement

getFrequencyElement

getFrequencyUnitElement

getFormElement

getDurationElement

getRouteElement

getDrugChangeStatusElement

getStrengthElement

getConfidenceScoreElement

parseIntValue

parseDoubleValue

convertFromTextToNum

convertToChangeStatus

getDosageBegin

getDosageEnd

getFrequencyBegin

getFrequencyEnd

getFUBegin

getFUENd

getFormBegin

getFormEnd

getDuratationBegin

getDuratationEnd

getRouteBegin

getRouteEnd

getStrengthUnitBegin

getStrengthUnitEnd

getStrengthBegin

getStrengthEnd

getChangeStatusBegin

getChangeStatusEnd

indexOfRegex