ctakes type system - apache/ctakes GitHub Wiki
Differentiates a token as being a word rather than a punctuation, symbol, newline, contraction, or number. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.WordToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| capitalization | uima.cas.Integer | ||
| numPosition | uima.cas.Integer | ||
| suggestion | uima.cas.String | ||
| canonicalForm | uima.cas.String |
A supertype for tokens subsuming word, punctuation, symbol, newline, contraction, or number. Includes parts of speech, which are grammatical categories, e.g., noun (NN) or preposition (IN) that use Penn Treebank tags with a few additions. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.BaseToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| tokenNumber | uima.cas.Integer | ||
| normalizedForm | uima.cas.String | ||
| partOfSpeech | uima.cas.String | ||
| lemmaEntries | uima.cas.FSList | Lemma |
Differentiates a token as being a contraction rather than a punctuation, symbol, newline, word, or number. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.ContractionToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
No variables specific to this type.
Equivalent to cTAKES: org.apache.ctakes.typesystem.type.DocumentID, but its supertype changed to uima.cas.TOP
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| documentID | uima.cas.String |
Can specify a prefix to a document ID. Useful for directory tree retention.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| documentIdPrefix | uima.cas.String |
Can specify the full path to a document source. Useful for directory retention.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| documentPath | uima.cas.String |
Stores a lemma (canonical form of a token). Inherits from uima.cas.TOP, allowing for reuse of standardized forms across the CAS. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Lemma
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| key | uima.cas.String | ||
| posTag | uima.cas.String |
Differentiates a token as being a newline rather than a punctuation, symbol, contraction, word, or number. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.NewlineToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
No variables specific to this type.
Differentiates a token as being a number rather than a punctuation, symbol, newline, word, or contraction. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.NumToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| numType | uima.cas.Integer |
Ontologies (e.g., SNOMED-CT) provide an expert semantic representation for concepts. They typically assign a code to a concept and normalize across various textual representations of that concept. IdentifiedAnnotation and Elements may point to these normalized concept representations to indicate clinical concepts. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.OntologyConcept
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| codingScheme | uima.cas.String | ||
| code | uima.cas.String | ||
| oid | uima.cas.String | ||
| oui | holds the rxnorm unique identifier for a given drug mention. TODO: change this attribute because of name clash (UMLS/SNOMED) | uima.cas.String | |
| score | Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, the score represents how similar this sense is to surrounding senses (higher scores = more likely to be the correct sense) | uima.cas.Double | |
| disambiguated | Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, then the OntologyConcept with disambiguated=true is the most likely sense | uima.cas.Boolean |
Differentiates a token as being punctuation rather than a contraction, symbol, newline, word, or number. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.PunctuationToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
No variables specific to this type.
A section of a clinical text, e.g., Diagnosis, Current Medications, Problem List. Different segments often have differing sublanguages and clinical relevance. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Segment
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.String | ||
| preferredText | preferredText is the normalized/resolved section name. Normally, this is populated by the Sectionizer and would contain the HL7/CCDA section name. | uima.cas.String | |
| tagText | tagText is the unresolved section name; the raw text in the document indicating (tagging) the section. Basically covered text of the section's tag. | uima.cas.String |
Sentences may or may not be fully-formed and grammatical. They form the unit of analysis for some downstream components (e.g., constituency parsers). Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Sentence
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| sentenceNumber | uima.cas.Integer | ||
| segmentId | uima.cas.String |
Differentiates a token as being a symbol rather than a punctuation, contraction, newline, word, or number. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.SymbolToken
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BaseToken
No variables specific to this type.
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. For example, "pain" would have a cui=C0030193 and tui=T184. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.UmlsConcept
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: OntologyConcept
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| cui | uima.cas.String | ||
| tui | uima.cas.String | ||
| preferredText | preferredText is the preferred term. normally his is the UMLS preferred name. | uima.cas.String |
Chunks are syntactic groupings of tokens, and are the results of a shallow parser (chunker). Possible chunkTypes follow Penn Treebank guidelines, e.g., noun phrase (NP) or prepositional phrase (PP) Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.Chunk
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| chunkType | uima.cas.String |
A noun phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.NP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
An adjective phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADJP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
An adverb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADVP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A phrase-level conjunction Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.CONJP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
An interjection Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.INTJ
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A list item, usually intra-sentential Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.LST
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A prepositional phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A particle, e.g., "out" in "rule out" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PRT
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A subordinate clause Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.SBAR
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
An unlike coordinating phrase, e.g., a NP and a PP conjoined via "and" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.UCP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
A verb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.VP
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Chunk
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.FractionAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.DateAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.TimeAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RangeAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
Contextual information of an entity. Equivalent to cTAKES: edu.mayo.bmi.uima.context.type.ContextAnnotation
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| FocusText | uima.cas.String | ||
| Scope | uima.cas.String |
Defines a window within which dictionary terms may match. An auxiliary spanned type. Equivalent to cTAKES: edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
No variables specific to this type.
Means by which the medication was taken or administered. Value set includes Topical, Enteral_Oral, Parenteral_Intravenous, Other, undetermined, etc.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Form of this medication. Value set includes tablet, capsule, liquid, inhalant, gel, other, etc.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Strength indicates the strength number and unit of the prescribed drug. E.g. "5 mg" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | the unit of measurement | uima.cas.String |
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"
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Dosage indicates how much of a prescribed drug should be taken. E.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
How often a medication should be used. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | The periodic unit used, e.g day, month, hour, etc. | uima.cas.String |
Status refers to the whether the medication is currently being taken or not. Value set: start, stop, increase, decrease, no change.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | Indicates the change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'. | uima.cas.String |
Corresponds to the UMLS Devices semantic group: medical device and research device. Example: arterial line has a Medical Device semantic type. This is qualifying information on how a procedure was done.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
The way or the equipment used to give or administration something (medication, test). This corresponds to the Procedures UMLS semantic group. More qualifying information on how the procedure was done.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Quantitative results of a laboratory, with number and unit.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | uima.cas.String |
Holds a narrative (i.e. string) reference range
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.). This is finer-grained to allow combinations of values.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Value set: unmarked (default), left, right, bilateral
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
An indication of progress or decline of a condition. Value set: unmarked (default), changed, increased, decreased, improved, worsened, resolved
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
An explicitly-mentioned indication of the seriousness of a condition. Value Set: unmarked (default), severe, moderate, slight
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
A body part or area, corresponding to the UMLS semantic group of Anatomy. An Entity based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Entity
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| bodyLaterality | org.apache.ctakes.typesystem.type.refsem.BodyLaterality | ||
| bodySide | org.apache.ctakes.typesystem.type.refsem.BodySide |
This is an Event from the UMLS semantic group of Chemicals and Drugs, pruned by RxNORM source. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Event
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| medicationFrequency | org.apache.ctakes.typesystem.type.refsem.MedicationFrequency | ||
| medicationDuration | org.apache.ctakes.typesystem.type.refsem.MedicationDuration | ||
| medicationRoute | org.apache.ctakes.typesystem.type.refsem.MedicationRoute | ||
| medicationStatusChange | org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange | ||
| medicationDosage | org.apache.ctakes.typesystem.type.refsem.MedicationDosage | ||
| medicationStrength | org.apache.ctakes.typesystem.type.refsem.MedicationStrength | ||
| medicationForm | org.apache.ctakes.typesystem.type.refsem.MedicationForm | ||
| startDate | org.apache.ctakes.typesystem.type.refsem.Date | ||
| endDate | org.apache.ctakes.typesystem.type.refsem.Date | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalRelation | ||
| dosageCount | org.apache.ctakes.typesystem.type.refsem.DosageCount | ||
| dose | org.apache.ctakes.typesystem.type.refsem.Dose | ||
| totalDose | org.apache.ctakes.typesystem.type.refsem.TotalDose | ||
| form | org.apache.ctakes.typesystem.type.refsem.Form | ||
| route | org.apache.ctakes.typesystem.type.refsem.Route | ||
| frequency | org.apache.ctakes.typesystem.type.refsem.Frequency | ||
| duration | org.apache.ctakes.typesystem.type.refsem.Duration | ||
| statusChange | org.apache.ctakes.typesystem.type.refsem.StatusChange |
This is an Event from the UMLS semantic group of Procedures (except that Laboratory procedures are separate). Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Event
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| bodyLaterality | org.apache.ctakes.typesystem.type.refsem.BodyLaterality | ||
| bodySide | org.apache.ctakes.typesystem.type.refsem.BodySide | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOf | ||
| procedureDevice | org.apache.ctakes.typesystem.type.refsem.ProcedureDevice | ||
| endTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| method | org.apache.ctakes.typesystem.type.refsem.ProcedureMethod | ||
| startTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalRelation | ||
| anatomicalSite | Anatomical site replaces the circular bodyLocation relation plus bodyLaterality and bodySide. | org.apache.ctakes.typesystem.type.refsem.AnatomicalSite | |
| dosageCount | org.apache.ctakes.typesystem.type.refsem.DosageCount | ||
| dose | org.apache.ctakes.typesystem.type.refsem.Dose | ||
| totalDose | org.apache.ctakes.typesystem.type.refsem.TotalDose | ||
| form | org.apache.ctakes.typesystem.type.refsem.Form | ||
| route | org.apache.ctakes.typesystem.type.refsem.Route | ||
| frequency | org.apache.ctakes.typesystem.type.refsem.Frequency | ||
| duration | org.apache.ctakes.typesystem.type.refsem.Duration | ||
| statusChange | org.apache.ctakes.typesystem.type.refsem.StatusChange |
This is an Event from the UMLS semantic group of Sign or Symptom. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Event
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| alleviatingFactor | org.apache.ctakes.typesystem.type.relation.ElementRelation | ||
| bodyLaterality | org.apache.ctakes.typesystem.type.refsem.BodyLaterality | ||
| bodySide | org.apache.ctakes.typesystem.type.refsem.BodySide | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOf | ||
| course | org.apache.ctakes.typesystem.type.refsem.Course | ||
| duration | org.apache.ctakes.typesystem.type.relation.TemporalRelation | ||
| endTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| exacerbatingFactor | org.apache.ctakes.typesystem.type.relation.ElementRelation | ||
| severity | uima.cas.String | ||
| startTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalRelation |
This is an Event from the UMLS semantic group of Disorders (except that Sign and Symptom types are separate). Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Event
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| alleviatingFactor | org.apache.ctakes.typesystem.type.relation.ElementRelation | ||
| associatedSignSymptom | org.apache.ctakes.typesystem.type.relation.ManifestationOf | ||
| bodyLaterality | org.apache.ctakes.typesystem.type.refsem.BodyLaterality | ||
| bodySide | org.apache.ctakes.typesystem.type.refsem.BodySide | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOf | ||
| course | org.apache.ctakes.typesystem.type.refsem.Course | ||
| duration | org.apache.ctakes.typesystem.type.relation.TemporalRelation | ||
| endTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| exacerbatingFactor | org.apache.ctakes.typesystem.type.relation.ElementRelation | ||
| startTime | org.apache.ctakes.typesystem.type.refsem.Time | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalRelation |
This is an Event from the UMLS semantic group of Laboratory Procedures. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Event
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| abnormalInterpretation | org.apache.ctakes.typesystem.type.relation.DegreeOf | ||
| deltaFlag | org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag | ||
| labValue | org.apache.ctakes.typesystem.type.refsem.LabValue | ||
| ordinalInterpretation | org.apache.ctakes.typesystem.type.relation.DegreeOf | ||
| referenceRangeNarrative | org.apache.ctakes.typesystem.type.refsem.LabReferenceRange |
A basic semantic unit that refers to something in the real world, including Entities, Events, Attributes, Dates. Element inherits from uima.cas.TOP to combine textual mentions of these real-world objects.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.Integer | ||
| ontologyConcept | org.apache.ctakes.typesystem.type.refsem.OntologyConcept | ||
| mentions | uima.cas.FSArray | IdentifiedAnnotation | |
| discoveryTechnique | uima.cas.Integer | ||
| confidence | uima.cas.Double | ||
| conditional | uima.cas.Boolean | ||
| generic | uima.cas.Boolean | ||
| subject | uima.cas.String | ||
| polarity | uima.cas.Integer | ||
| uncertainty | uima.cas.Integer | ||
| historyOf | uima.cas.Integer |
A normalized form for Time annotations. Inherits from Element, but some fields may be unused.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Element
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| normalizedForm | uima.cas.String |
A normalized form for dates, namely with day, month, and year. A subtype of Element but may not use all inherited attributes.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Element
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| day | uima.cas.String | ||
| month | uima.cas.String | ||
| year | uima.cas.String |
A real-world event; similar to Entity, but may bear some temporal properties and relationships. In the constrained clinical context, many concepts are discussed as instances with some temporal component, e.g., Medications, Labs.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Element
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| properties | org.apache.ctakes.typesystem.type.refsem.EventProperties |
A real-world entity such as a body part. For example, multiple Procedures may have the same AnatomicalSite entity for their locations.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Element
No variables specific to this type.
The semantic encapsulation of a modifer. E.g., for Clinical Elements, Attributes may be used to specify Body Side for a Procedure.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Element
No variables specific to this type.
A set of mostly temporal properties that are unique to Events.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| contextualModality | uima.cas.String | ||
| contextualAspect | uima.cas.String | ||
| permanence | uima.cas.String | ||
| category | Type of Event. | uima.cas.String | |
| aspect | uima.cas.String | ||
| docTimeRel | uima.cas.String | ||
| degree | uima.cas.String | ||
| polarity | uima.cas.Integer |
A superclass for semantic relationships between Elements. For example, one might consider TemporalRelations or UMLSRelations between a Medication and a Disorder. The "category" feature indicates what kind of relation it is.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.Integer | ||
| category | uima.cas.String | ||
| discoveryTechnique | uima.cas.Integer | ||
| confidence | uima.cas.Double | ||
| polarity | uima.cas.Integer | ||
| uncertainty | uima.cas.Integer | ||
| conditional | Whether the relation is conditional/hypothetical. Example: "If the patient's tumor returns, we can treat it with Oxaliplatin." This instantiates a manages/treats relation which should be marked as conditional=true, with the "if" marked as the cue. | uima.cas.Boolean |
Relations are like lines connecting two or more endpoints. RelationArguments are used as endpoints that are text spans via the "argument" feature. The directed relations should specify a "role" feature.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.Integer | ||
| argument | uima.tcas.Annotation | ||
| role | uima.cas.String | ||
| participatesIn | uima.cas.FSList | Relation |
A super-type for relationships between two spans of text.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| arg1 | org.apache.ctakes.typesystem.type.relation.RelationArgument | ||
| arg2 | org.apache.ctakes.typesystem.type.relation.RelationArgument |
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| members | A super-type for relationships between multiple spans of text. | uima.cas.FSList | RelationArgument |
A biomedical relationship between two spans of text that have been mapped to UMLS concepts. Inherits "category" from Relation, with values such as affects, causes, complicates, contraindicates, degree_of, etc.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
A coreference pair, with antecedent as arg1 and anaphor as arg2
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
A super-type referring to real-world semantic relationships, e.g., TemporalRelations between two Events.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| arg1 | org.apache.ctakes.typesystem.type.refsem.Element | ||
| arg2 | org.apache.ctakes.typesystem.type.refsem.Element |
A real-world relationship between an Element and an Attribute.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| arg1 | org.apache.ctakes.typesystem.type.refsem.Element | ||
| arg2 | org.apache.ctakes.typesystem.type.refsem.Attribute |
Based on ISO TimeML's TLINK.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
A UMLS relation between an attribute and an entity/event.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: AttributeRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: ElementRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
A UMLS relation between clinical elements.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: BinaryTextRelation
No variables specific to this type.
Demographic information about the patient in a clinical document. Typically comes from structured metadata.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| birthDate | uima.cas.String | ||
| deathDate | uima.cas.String | ||
| gender | uima.cas.String | ||
| firstName | uima.cas.String | ||
| middleName | uima.cas.String | ||
| lastName | uima.cas.String | ||
| firstNameSoundex | uima.cas.String | ||
| lastNameSoundex | uima.cas.String |
Information about the caregiving setting for the clinical document. Typically comes from structured metadata.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| noteTypeCode | uima.cas.String | ||
| noteSubTypeCode | uima.cas.String | ||
| authorSpecialty | uima.cas.String | ||
| documentStandard | uima.cas.String | ||
| sourceInstanceId | uima.cas.String | ||
| sourceRevisionNbr | uima.cas.Integer | ||
| sourceRevisionDate | uima.cas.String | ||
| sourceOriginalDate | uima.cas.String | ||
| sourceInstitution | uima.cas.String | ||
| sourceEncounterId | uima.cas.String | ||
| sourceApplication | uima.cas.String |
Structured data that captures information about the document, patient, or context of the clinical text.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| patientIdentifier | Represents a text identifier for the patient. | uima.cas.String | |
| patientID | patientID is a simple long. Could be renamed to patientNum. | uima.cas.Long | |
| providerID | uima.cas.LongArray | ||
| sourceData | org.apache.ctakes.typesystem.type.structured.SourceData | ||
| demographics | org.apache.ctakes.typesystem.type.structured.Demographics |
A Penn Treebank-style tree node. Conforms to PTB 2.0 guidelines.
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| nodeType | uima.cas.String | ||
| nodeValue | uima.cas.String | ||
| leaf | uima.cas.Boolean | ||
| parent | org.apache.ctakes.typesystem.type.syntax.TreebankNode | ||
| children | uima.cas.FSArray | TreebankNode | |
| nodeTags | uima.cas.StringArray | ||
| headIndex | The head index tracks the index into the word tokens which is the syntactic head of a phrase. | uima.cas.Integer |
A Penn Treebank Node; as a terminal, there is an associated word, and the index of the word is a feature.
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: TreebankNode
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| index | The index of this node in the top node's list of terminals. | uima.cas.Integer | |
| tokenIndex | The tokenIndex of a terminal is n, where the terminal is the nth token in a sentence. The value -1 means that this terminal does not correspond to a token (because it is a trace.) We assume that each token corresponds to a terminal. | uima.cas.Integer |
A Penn Treebank Node; as the top node, this stores the whole subsumed sentence's parse tree as a string. It also stores all the terminals, allowing for traversal of the tree bottom-up (top-down is implied through the TreebankNode's 'children' attribute).
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: TreebankNode
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| treebankParse | A bracketed sentence string representing the parse tree. | uima.cas.String | |
| terminals | Stores the terminal nodes of the parse tree. This allows for bottom-up traversal of a tree. | uima.cas.FSArray | TerminalTreebankNode |
A dependency parser node in the CONLL-X format, namely, where each node is a token with 10 fields.
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | The token's position in the sentence. The ROOT node, present in every dependency parse, has id=0. | uima.cas.Integer | |
| form | uima.cas.String | ||
| lemma | uima.cas.String | ||
| cpostag | uima.cas.String | ||
| postag | uima.cas.String | ||
| feats | uima.cas.String | ||
| head | org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode | ||
| deprel | uima.cas.String | ||
| phead | org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode | ||
| pdeprel | uima.cas.String |
Stanford dependencies provide a representation of grammatical relations between words in a sentence. Stanford dependencies are triplets: name of the relation, governor and dependent.
Package Name: org.apache.ctakes.typesystem.type.syntax
Parent Type: BinaryTextRelation
No variables specific to this type.
Any span of text that has been discovered or flagged for some reason, such as a Named Entity. Allows for mapping to an ontology. Generalized from cTAKES: org.apache.ctakes.typesystem.type.IdentifiedAnnotation.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.Integer | ||
| ontologyConceptArr | uima.cas.FSArray | OntologyConcept | |
| typeID | The type of named entity (e.g. drug, disorder, ...) | uima.cas.Integer | |
| segmentID | uima.cas.String | ||
| sentenceID | contains the sentence id of the sentence that contains the NE's text span | uima.cas.String | |
| discoveryTechnique | uima.cas.Integer | ||
| confidence | The confidence of the annotation. | uima.cas.Float | |
| polarity | uima.cas.Integer | ||
| uncertainty | uima.cas.Integer | ||
| conditional | uima.cas.Boolean | ||
| generic | uima.cas.Boolean | ||
| subject | uima.cas.String | ||
| historyOf | uima.cas.Integer | ||
| originalText | The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation. If the covered text is from disjoint spans, they are separated by a delimeter. | uima.cas.FSArray |
A cue phrase indicating potential negation, uncertainty, or conditional
Package Name: org.apache.ctakes.typesystem.type.temporary.assertion
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.Integer | ||
| cuePhraseCategory | uima.cas.String | ||
| cuePhraseAssertionFamily | which assertion family this cue phrase belongs to (negation, uncertainty, or conditional) | uima.cas.String | |
| cuePhraseFirstWord | first word of cue phrase | uima.cas.String | |
| cuePhrase | cue phrase itself (from lookup list) | uima.cas.String |
A text string (IdentifiedAnnotation) that refers to an Entity.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| entity | org.apache.ctakes.typesystem.type.refsem.Entity |
A text string (IdentifiedAnnotation) that refers to an Event.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| event | org.apache.ctakes.typesystem.type.refsem.Event |
Deprecated. As of cTAKEs 3.1, see org.apache.ctakes.typesystem.type.textsem.MedicationMention.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| medicationFrequency | org.apache.ctakes.typesystem.type.refsem.MedicationFrequency | ||
| medicationDuration | org.apache.ctakes.typesystem.type.refsem.MedicationDuration | ||
| medicationRoute | org.apache.ctakes.typesystem.type.refsem.MedicationRoute | ||
| medicationStatusChange | org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange | ||
| medicationDosage | org.apache.ctakes.typesystem.type.refsem.MedicationDosage | ||
| medicationStrength | org.apache.ctakes.typesystem.type.refsem.MedicationStrength | ||
| medicationForm | org.apache.ctakes.typesystem.type.refsem.MedicationForm | ||
| startDate | org.apache.ctakes.typesystem.type.refsem.Date | ||
| endDate | org.apache.ctakes.typesystem.type.refsem.Date |
A text string (IdentifiedAnnotation) that refers to a Time (i.e., TIMEX3).
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| date | org.apache.ctakes.typesystem.type.refsem.Date | ||
| time | org.apache.ctakes.typesystem.type.refsem.Time | ||
| timeClass | DATE, DURATION, QUANTIFIER, PREPOSTEXP, etc. | uima.cas.String |
A text string (IdentifiedAnnotation) that refers to an Attribute.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| normalizedForm | org.apache.ctakes.typesystem.type.refsem.Attribute | ||
| category | uima.cas.String |
Predicates are typically verbs and may participate in SemanticRoleRelations. Follows PropBank standards with a few clinical additions.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| relations | uima.cas.FSList | SemanticRoleRelation | |
| frameSet | uima.cas.String |
SemanticArguments are used for predicate-argument structures (SemanticRoleRelations). The "label" features should contain the type of semantic role (e.g., ARG0, ARGM) that this argument has w.r.t. the predicate.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| relation | org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation | ||
| label | uima.cas.String |
Predicate-argument structure used for semantic role labeling output.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| predicate | org.apache.ctakes.typesystem.type.textsem.Predicate | ||
| argument | org.apache.ctakes.typesystem.type.textsem.SemanticArgument |
A text span corresponding to a paragraph, typically containing multiple sentences.
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
No variables specific to this type.
A semi-structured text span, containing other Annotations (typically Sentences, other Lists, etc).
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| id | uima.cas.String | ||
| items | uima.cas.FSList | Annotation |
A text span corresponding to a list entry, typically a single line in a multiline List.
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
No variables specific to this type.
An Attribute-Value tuple. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Property
Package Name: org.apache.ctakes.typesystem.type.util
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| attribute | uima.cas.String | ||
| value | uima.cas.String |
A brute force "hash" that stores multiple Pairs in a list. Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Properties
Package Name: org.apache.ctakes.typesystem.type.util
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| pairs | uima.cas.FSArray | Pair |
A brute force probability distribution for discrete variables.
Package Name: org.apache.ctakes.typesystem.type.util
Parent Type: Pairs
No variables specific to this type.
Package Name: org.apache.ctakes.typesystem.type.structured
Parent Type: TOP
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| label | uima.cas.String |
Means by which the medication was taken or administered. Value set includes Topical, Enteral_Oral, Parenteral_Intravenous, Other, undetermined, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Form of this medication. Value set includes tablet, capsule, liquid, inhalant, gel, other, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Strength indicates the strength number and unit of the prescribed drug. E.g. "5 mg" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
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"
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Dosage indicates how much of a prescribed drug should be taken. E.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
How often a medication should be used. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Status refers to the whether the medication is currently being taken or not. Value set: start, stop, increase, decrease, no change.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Corresponds to the UMLS Devices semantic group: medical device and research device. Example: arterial line has a Medical Device semantic type. This is qualifying information on how a procedure was done.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
The way or the equipment used to give or administration something (medication, test). This corresponds to the Procedures UMLS semantic group. More qualifying information on how the procedure was done.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Quantitative results of a laboratory, with number and unit.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Holds a narrative (i.e. string) reference range
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.). This is finer-grained to allow combinations of values.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Value set: unmarked (default), left, right, bilateral
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
An indication of progress or decline of a condition. Value set: unmarked (default), changed, increased, decreased, improved, worsened, resolved
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
An explicitly-mentioned indication of the seriousness of a condition. Value Set: unmarked (default), severe, moderate, slight
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Used to indicate that a procedure or assertion did not occur or does not exist. If indicated, negation is present and polarity should be -1. If not indicated, negation is not present and polarity should be +1 by default.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
The Conditional modifier refers to mentions which could exist under certain circumstances. If indicated, there are conditions under which an associated Named Entity mention might not be truly asserted.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
An introduction of a measure of doubt into a statement. If indicated, there is uncertainty.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
The Generic modifier indicates that a named entity mention is generic, i.e., not related to the instance of a disorder, sign/symptom, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
The person the observation is on, i.e., a Person mention. This modifier refers to the entity experiencing the disorder.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
An indication of explicit mentioning of a past history. The indicator captures only very explicit mentions of historicity.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
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.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Indication of whether the medication is mentioned in the context of Allergies.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
Signals that the lab value was estimated, e.g., "GFR (estimated): 81". True means that there is an indicator signalling that there was an estimation of the value.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| indicated | uima.cas.Boolean |
A text string that refers to a (AnatomicalSite) Entity. A body part or area, corresponding to the UMLS semantic group of Anatomy. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EntityMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| bodyLaterality | org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier | ||
| bodySide | org.apache.ctakes.typesystem.type.textsem.BodySideModifier |
A text string that refers to a (Medication) Event. This is an Event from the UMLS semantic group of Chemicals and Drugs, pruned by RxNORM source. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| medicationAllergy | org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier | ||
| medicationFrequency | org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier | ||
| medicationDuration | org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier | ||
| medicationRoute | org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier | ||
| medicationStatusChange | org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier | ||
| medicationDosage | org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier | ||
| medicationStrength | org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier | ||
| medicationForm | org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier | ||
| startDate | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| endDate | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation | ||
| dosageCount | org.apache.ctakes.typesystem.type.textsem.DosageCountModifier | ||
| dose | org.apache.ctakes.typesystem.type.textsem.DoseModifier | ||
| totalDose | org.apache.ctakes.typesystem.type.textsem.TotalDoseModifier | ||
| form | org.apache.ctakes.typesystem.type.textsem.FormModifier | ||
| route | org.apache.ctakes.typesystem.type.textsem.RouteModifier | ||
| frequency | org.apache.ctakes.typesystem.type.textsem.FrequencyModifier | ||
| duration | org.apache.ctakes.typesystem.type.textsem.DurationModifier | ||
| statusChange | org.apache.ctakes.typesystem.type.textsem.StatusChangeModifier |
A text string that refers to a (Procedure) Event. This is from the UMLS semantic group of Procedures (except that Laboratory procedures are separate). Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| bodyLaterality | org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier | ||
| bodySide | org.apache.ctakes.typesystem.type.textsem.BodySideModifier | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation | ||
| procedureDevice | org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier | ||
| endTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| method | org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier | ||
| startTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation | ||
| anatomicalSite | Anatomical site mention replaces the circular bodyLocation relation plus bodyLaterality and bodySide. | org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention | |
| dosageCount | org.apache.ctakes.typesystem.type.textsem.DosageCountModifier | ||
| dose | org.apache.ctakes.typesystem.type.textsem.DoseModifier | ||
| totalDose | org.apache.ctakes.typesystem.type.textsem.TotalDoseModifier | ||
| form | org.apache.ctakes.typesystem.type.textsem.FormModifier | ||
| route | org.apache.ctakes.typesystem.type.textsem.RouteModifier | ||
| frequency | org.apache.ctakes.typesystem.type.textsem.FrequencyModifier | ||
| duration | org.apache.ctakes.typesystem.type.textsem.DurationModifier | ||
| statusChange | org.apache.ctakes.typesystem.type.textsem.StatusChangeModifier |
A text string that refers to a (SignSymptom) Event. This is from the UMLS semantic group of Sign or Symptom. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| alleviatingFactor | org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation | ||
| bodyLaterality | org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier | ||
| bodySide | org.apache.ctakes.typesystem.type.textsem.BodySideModifier | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation | ||
| course | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation | ||
| duration | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation | ||
| endTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| exacerbatingFactor | org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation | ||
| severity | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation | ||
| startTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation |
A text string that refers to a (DiseaseDisorder) Event. This is from the UMLS semantic group of Disorders (except that Sign and Symptom types are separate). Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| alleviatingFactor | org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation | ||
| associatedSignSymptom | org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation | ||
| bodyLaterality | org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier | ||
| bodySide | org.apache.ctakes.typesystem.type.textsem.BodySideModifier | ||
| bodyLocation | org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation | ||
| course | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation | ||
| duration | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation | ||
| endTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| exacerbatingFactor | org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation | ||
| startTime | org.apache.ctakes.typesystem.type.textsem.TimeMention | ||
| relativeTemporalContext | org.apache.ctakes.typesystem.type.relation.TemporalTextRelation | ||
| severity | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation |
A text string that refers to a (Lab) Event. This is from the UMLS semantic group of Laboratory Procedures. Based on generic Clinical Element Models (CEMs)
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: EventMention
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| abnormalInterpretation | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation | ||
| deltaFlag | org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier | ||
| labValue | org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation | ||
| ordinalInterpretation | org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation | ||
| referenceRangeNarrative | org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier |
A type for representing text spans that can potentially be linked together via coreference.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: IdentifiedAnnotation
No variables specific to this type.
A relation between a chain relation and an identified annotation mention. Useful for relating a new mention to a collection of previous mentions, e.g., in coreference resolution.
Package Name: org.apache.ctakes.typesystem.type.relation
Parent Type: Relation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| cluster | org.apache.ctakes.typesystem.type.relation.CollectionTextRelation | ||
| mention | org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation |
An annotation within a text span for an Episode.
Package Name: org.apache.ctakes.typesystem.type.textspan
Parent Type: Annotation
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| episodeType | uima.cas.String |
How many Medication or Procedure Dosage expressions. e.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Dose indicates the 'strength' number and unit of a medication or procedure. e.g. 5 mg, 100 cGy, etc.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | the unit of dose measurement | uima.cas.String |
Indicates the total dose number and unit of a medication or procedure. e.g. Two 5mg tabs = 10mg.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | the unit of dose measurement | uima.cas.String |
Form of a medication or procedure. e.g. tablet, brachytherapy, etc.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
Means by which the medication or procedure was taken or administered. e.g. Oral, beam path, etc.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | uima.cas.String |
How often a Medication or Procedure should occur. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | The periodic unit used, e.g day, month, hour, etc. | uima.cas.String |
Amount of time over which a medication or procedure should occur. e.g. 2 weeks
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| number | uima.cas.String | ||
| unit | the unit of time measurement. e.g day, month, hour, etc. | uima.cas.String |
Does this Medication or Procedure represent a change in state. e.g. start of use, increase of strength, no change.
Package Name: org.apache.ctakes.typesystem.type.refsem
Parent Type: Attribute
| Feature Name | Description | Type | Element Type |
|---|---|---|---|
| value | Indicates the change status of 'stop', 'start', 'increase', 'decrease', 'noChange', 'boost'. | uima.cas.String |
How many Medication or Procedure Dosage expressions. e.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Dose indicates the 'strength' number and unit of a medication or procedure. e.g. 5 mg, 100 cGy, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Indicates the total dose number and unit of a medication or procedure. e.g. Two 5mg tabs = 10mg.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Form of a medication or procedure. e.g. tablet, brachytherapy, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Means by which the medication or procedure was taken or administered. e.g. Oral, beam path, etc.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
How often a Medication or Procedure should occur. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Amount of time over which a medication or procedure should occur. e.g. 2 weeks
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.
Does this Medication or Procedure represent a change in state. e.g. start of use, increase of strength, no change.
Package Name: org.apache.ctakes.typesystem.type.textsem
Parent Type: Modifier
No variables specific to this type.