An adjective phrase
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.ADJP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
ADJP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP
An adverb phrase
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.ADVP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
ADVP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A cue phrase indicating potential negation, uncertainty,
or conditional
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
performs the patient-level smoking status classification based on document-level classification
each patient is assigned only one final smoking status
RULE:
If exists only U assign U
Else if exist N and there is no PCS assign N
Else if exist S and there is no PC assign S
Else if exist P or C (can be both)
If exists either P or C assign P or C respectively
Else if exist both P and C
If(C freq >= P freq) assign C
Else assign P
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Value set: unmarked (default), left, right, bilateral
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
BodySide() -
Constructor for class org.apache.ctakes.typesystem.type.refsem.BodySide
Value set: unmarked (default), left, right, bilateral
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A phrase-level conjunction
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.CONJP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
CONJP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP
A coreference pair, with antecedent as arg1 and anaphor
as arg2
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.DateAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
DocumentID() -
Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
Equivalent to cTAKES:
org.apache.ctakes.typesystem.type.DocumentID, but its supertype
changed to uima.cas.TOP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
DocumentID() -
Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentID
Equivalent to cTAKES:
org.apache.ctakes.typesystem.type.DocumentID, but its supertype
changed to uima.cas.TOP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.FractionAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
indexed getter for originalText - gets an indexed value - The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
An interjection
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.INTJ
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
INTJ() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ
Test result interpretations organized in a valued list
e.g., "rare cells seen" or "few cells seen" in urinalysis, now
combined with very_abnormal and abnormal.
Test result interpretations organized in a valued list
e.g., "rare cells seen" or "few cells seen" in urinalysis, now
combined with very_abnormal and abnormal.
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A list item, usually intra-sentential
Equivalent to
cTAKES: edu.mayo.bmi.uima.chunker.type.LST
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
LST() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
Never called.
LST(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
Internal - constructor used by generator
LST(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
LST(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
keywordsFile and stopwordsFile must point to the files in the resources
dataFile is your own sentence-level data in the format (class_label: C,
P, S): sentence|class_label sentence|class_label ...
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
The amount of time after which a medication should stop
being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2
weeks"
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
The amount of time after which a medication should stop
being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2
weeks"
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
The amount of time after which a medication should stop
being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2
weeks"
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
The amount of time after which a medication should stop
being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2
weeks"
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
This context analyzer provides code that is shared by the
StatusContextAnalyzer and NegationContextAnalyzer which are both analyzers
that examine the contexts surrounding named entity annotations.
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project
to use "NonSmokerNamedEntityAnnotation" instead of NamedEntityAnnotation
A noun phrase
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.NP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
NP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
Never called.
NP(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
Internal - constructor used by generator
NP(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
NP(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
O() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.O
Never called.
O(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.O
Internal - constructor used by generator
O(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.O
O(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.O
Patient-level smoking status classification used for the AMIA 2009 paper
From PatientLevelSmokingStatus_Jan09.java revised frequency based except for assigning past smoker
if exists only past and non-smoker
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A prepositional phrase
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.PP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
PP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
Never called.
PP(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
Internal - constructor used by generator
PP(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
PP(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
A particle, e.g., "out" in "rule out"
Equivalent to
cTAKES: edu.mayo.bmi.uima.chunker.type.PRT
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
PRT() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
Never called.
PRT(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
Internal - constructor used by generator
PRT(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
PRT(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.RangeAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A subordinate clause
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.SBAR
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
SBAR() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR
indexed setter for originalText - sets an indexed value - The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project
to use "SmokerNamedEntityAnnotation" instead of NamedEntityAnnotation
Represents classification related to the document
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Equivalent to cTAKES:
edu.mayo.bmi.uima.cdt.type.TimeAnnotation
Updated by JCasGen Thu Nov 28 10:34:47 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
An unlike coordinating phrase, e.g., a NP and a PP
conjoined via "and"
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.UCP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
UCP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
Never called.
UCP(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
Internal - constructor used by generator
UCP(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
UCP(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
An unlike coordinating phrase, e.g., a NP and a PP
conjoined via "and"
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.UCP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
Concepts in the Unified Medical Language System (UMLS)
Metathesaurus have a concept unique identifier (CUI) and a type
unique identifier (TUI, i.e., semantic type) which are curated,
normalized codes.
Concepts in the Unified Medical Language System (UMLS)
Metathesaurus have a concept unique identifier (CUI) and a type
unique identifier (TUI, i.e., semantic type) which are curated,
normalized codes.
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A verb phrase
Equivalent to cTAKES:
edu.mayo.bmi.uima.chunker.type.VP
Updated by JCasGen Thu Nov 28 10:34:46 CST 2013
XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
VP() -
Constructor for class org.apache.ctakes.typesystem.type.syntax.VP
Never called.
VP(int, TOP_Type) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.VP
Internal - constructor used by generator
VP(JCas) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.VP
VP(JCas, int, int) -
Constructor for class org.apache.ctakes.typesystem.type.syntax.VP