diff --git a/src/main/resources/archetype-resources/pom.xml b/src/main/resources/archetype-resources/pom.xml index 02c5d3c..80ce438 100644 --- a/src/main/resources/archetype-resources/pom.xml +++ b/src/main/resources/archetype-resources/pom.xml @@ -71,6 +71,27 @@ numeric-value-typesystem ${core-typesystems-version} + + de.averbis.textanalysis + named-entity-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + text-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + neural-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + evaluation-typesystem + ${core-typesystems-version} + + de.averbis.textanalysis @@ -190,27 +211,6 @@ - - org.codehaus.mojo - exec-maven-plugin - 1.6.0 - - - generate-ruta-template - process-classes - - java - - - ${package}.GenerateConfiguredDescriptorTemplate - test - - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml - - - - - org.apache.uima ruta-maven-plugin @@ -218,7 +218,7 @@ descriptors - process-classes + generate-sources generate @@ -229,7 +229,7 @@ **/*.ruta - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml + ${basedir}/src/main/resources/descriptor/GeneratedBasicEngine.xml ${project.build.directory}/generated-sources/ruta/descriptor ${project.build.directory}/generated-sources/ruta/descriptor RutaAnnotator @@ -248,6 +248,31 @@ + + + org.apache.uima + jcasgen-maven-plugin + ${uima-version} + + + generate-jcas-classes + generate-sources + + generate + + + + target/generated-sources/ruta/descriptor/${packageInPathFormat}/${rutaScriptName}RutaTypeSystem.xml + + + /**/BasicTypeSystem.xml + /**/InternalTypeSystem.xml + + true + + + + org.apache.maven.plugins maven-resources-plugin @@ -295,6 +320,7 @@ + org.apache.maven.plugins maven-dependency-plugin @@ -313,13 +339,13 @@ + org.apache.uima PearPackagingMavenPlugin ${uima-version} true - package @@ -334,35 +360,6 @@ - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.codehaus.mojo - exec-maven-plugin - [1.6.0,) - - java - - - - - - - - - - - - diff --git a/src/main/resources/archetype-resources/src/main/java/GenerateConfiguredDescriptorTemplate.java b/src/main/resources/archetype-resources/src/main/java/GenerateConfiguredDescriptorTemplate.java index 9959b2c..2b7bcc9 100644 --- a/src/main/resources/archetype-resources/src/main/java/GenerateConfiguredDescriptorTemplate.java +++ b/src/main/resources/archetype-resources/src/main/java/GenerateConfiguredDescriptorTemplate.java @@ -31,12 +31,17 @@ import org.apache.uima.ruta.engine.RutaEngine; import org.xml.sax.SAXException; +/** + * Helper class for manually generating a preconfigured descriptor template for the generated Ruta + * analysis engine descriptors + * + */ public class GenerateConfiguredDescriptorTemplate { public static void main(String[] args) throws ResourceInitializationException, FileNotFoundException, SAXException, IOException { - File outputFile = new File(args[0]); + File outputFile = new File("src/main/resources/descriptor/GeneratedBasicEngine.xml"); outputFile.getParentFile().mkdirs(); AnalysisEngineDescription description = AnalysisEngineFactory diff --git a/src/main/resources/archetype-resources/src/main/resources/descriptor/GeneratedBasicEngine.xml b/src/main/resources/archetype-resources/src/main/resources/descriptor/GeneratedBasicEngine.xml new file mode 100644 index 0000000..d5716b2 --- /dev/null +++ b/src/main/resources/archetype-resources/src/main/resources/descriptor/GeneratedBasicEngine.xml @@ -0,0 +1,6098 @@ + + + org.apache.uima.java + true + org.apache.uima.ruta.engine.RutaEngine + + org.apache.uima.ruta.engine.RutaEngine + Descriptor automatically generated by uimaFIT + unknown + org.apache.uima.ruta.engine + + + rules + + String + false + false + + + rulesScriptName + + String + false + true + + + mainScript + + String + false + false + + + scriptEncoding + + String + false + false + + + scriptPaths + + String + true + false + + + descriptorPaths + + String + true + false + + + resourcePaths + + String + true + false + + + additionalScripts + + String + true + false + + + additionalEngines + + String + true + false + + + additionalUimafitEngines + + String + true + false + + + additionalExtensions + + String + true + false + + + reloadScript + + Boolean + false + false + + + seeders + + String + true + false + + + defaultFilteredTypes + + String + true + false + + + removeBasics + + Boolean + false + false + + + dynamicAnchoring + + Boolean + false + false + + + lowMemoryProfile + + Boolean + false + false + + + simpleGreedyForComposed + + Boolean + false + false + + + greedyRuleElement + + Boolean + false + false + + + greedyRule + + Boolean + false + false + + + debug + + Boolean + false + false + + + debugWithMatches + + Boolean + false + false + + + debugAddToIndexes + + Boolean + false + false + + + debugOnlyFor + + String + true + false + + + profile + + Boolean + false + false + + + statistics + + Boolean + false + false + + + createdBy + + Boolean + false + false + + + strictImports + + Boolean + false + false + + + typeIgnorePattern + + String + false + false + + + dictRemoveWS + + Boolean + false + false + + + csvSeparator + + String + false + false + + + varNames + + String + true + false + + + varValues + + String + true + false + + + indexOnly + + String + true + false + + + reindexOnly + + String + true + false + + + indexOnlyMentionedTypes + + Boolean + false + true + + + reindexOnlyMentionedTypes + + Boolean + false + true + + + indexSkipTypes + + String + true + true + + + reindexSkipTypes + + String + true + true + + + indexAdditionally + + String + true + false + + + reindexAdditionally + + String + true + false + + + reindexUpdateMode + + String + false + true + + + validateInternalIndexing + + Boolean + false + true + + + emptyIsInvisible + + Boolean + false + false + + + modifyDataPath + + Boolean + false + false + + + inferenceVisitors + + String + true + false + + + maxRuleMatches + + Integer + false + false + + + maxRuleElementMatches + + Integer + false + false + + + + + rulesScriptName + + Anonymous + + + + scriptEncoding + + UTF-8 + + + + descriptorPaths + + + + + + resourcePaths + + + + + + additionalScripts + + + + + + additionalEngines + + + + + + additionalUimafitEngines + + + + + + additionalExtensions + + + + + + reloadScript + + false + + + + seeders + + + org.apache.uima.ruta.seed.TextSeeder + + + + + defaultFilteredTypes + + + org.apache.uima.ruta.type.SPACE + org.apache.uima.ruta.type.BREAK + org.apache.uima.ruta.type.MARKUP + + + + + removeBasics + + false + + + + dynamicAnchoring + + false + + + + lowMemoryProfile + + false + + + + simpleGreedyForComposed + + false + + + + greedyRuleElement + + false + + + + greedyRule + + false + + + + debug + + false + + + + debugWithMatches + + false + + + + debugAddToIndexes + + false + + + + debugOnlyFor + + + + + + profile + + false + + + + statistics + + false + + + + createdBy + + false + + + + strictImports + + false + + + + dictRemoveWS + + true + + + + csvSeparator + + ; + + + + varNames + + + + + + varValues + + + + + + indexOnly + + + uima.tcas.Annotation + + + + + reindexOnly + + + uima.tcas.Annotation + + + + + indexOnlyMentionedTypes + + false + + + + reindexOnlyMentionedTypes + + false + + + + indexSkipTypes + + + + + + reindexSkipTypes + + + + + + indexAdditionally + + + + + + reindexAdditionally + + + + + + reindexUpdateMode + + COMPLETE + + + + validateInternalIndexing + + false + + + + emptyIsInvisible + + true + + + + modifyDataPath + + false + + + + inferenceVisitors + + + + + + maxRuleMatches + + 2147483647 + + + + maxRuleElementMatches + + 2147483647 + + + + + + + de.averbis.extraction.types.Abbreviation + An abbreviation is a letter or group of letters, taken from a word or words. For + example, the word "abbreviation" can be abbreviated as "abbr." or "abbrev." + de.averbis.extraction.types.CoreAnnotation + + + fullForm + The full form of an abbreviation. The full form, for example for HLA could be + human leukocyte antigen. + uima.cas.String + + + textReference + Reference to the text span that contains the full form of the + abbreviation/acronym. + de.averbis.extraction.types.CoreAnnotation + + + definedHere + This feature is true if the abbreviation/acronym is defined for the first time in + the text, e.g. in "interleukin 2 (Il-2) receptor", it can be true only for locally introduced + abbreviations/acronyms. + uima.cas.Boolean + + + stems + Stems of the full form. + uima.cas.StringArray + true + + + segments + Segments of the full form. + uima.cas.StringArray + true + + + tokens + Token strings of the full form. + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Abstract + Semantic abstract section found in the text. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Category + Category meta information on the document or a region of this document (use the + context feature to identify which section this category refers to). E.g. language information of + the document text or language information of specific sections. + de.averbis.extraction.types.CoreAnnotation + + + group + The category group (e.g. HSG, language) to which from which the label belongs. + For language categorization the group might be "lang" and then the labels could be "en", "de", + "fr" etc. + uima.cas.String + + + label + The label of the category annotation. E.g. in the case that we identified + languages (de, en, fr, ...). + uima.cas.String + + + context + The text context which belongs to the given category annotation, e.g. Document, + Section, Sentence. + de.averbis.extraction.types.CoreAnnotation + + + rank + The rank of the current category with respect to the context. + uima.cas.Integer + + + + + de.averbis.extraction.types.Chunk + A general type for chunks (NPs, VPs, PPs etc.). + Note: there are 3 specific subtypes for common chunks: ChunkNP, ChunkVP, ChunkPP. + For all other chunk types (e.g., SBAR; ADJP etc.) use this general type! + de.averbis.extraction.types.CoreAnnotation + + + enclosedTokens + The Token annotations enclosed by this chunk. + uima.cas.Integer + + + head + The head entity on which this chunk grammatically depends. Example: in "Der Vater + des Kindes" is "der Vater" the head of "des Kindes". + de.averbis.extraction.types.CoreAnnotation + + + dependents + The entities which grammatically depend on this chunk. Example: in "Der Vater des + Kindes" is "des Kindes" the dependent of "Der Vater". + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + value + The specific chunk tag as returned by the chunker (e.g., "NP", "SBAR", "S" etc.). + uima.cas.String + + + + + de.averbis.extraction.types.ChunkNP + A noun phrase (e.g. "the strange bird"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.ChunkPP + A prepositional phrase (e.g. "in between"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.ChunkVP + A verb phrase (e.g. "has been thinking"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.Concept + A concept is a reference to an entry in a database, terminology, taxonomy, ontology + etc. + de.averbis.extraction.types.CoreAnnotation + + + dictCanon + Canonical form (preferred term). + uima.cas.String + + + enclosingSpan + The span that this concept is contained within (i.e. its sentence). + de.averbis.extraction.types.CoreAnnotation + + + negatedBy + Indicates which annotation negates the concept. + de.averbis.extraction.types.CoreAnnotation + + + partialMatch + Specifies if the annotation matches the complete context. + E.g. if coveredText is "Lungenabschnitte" and the generated Concept annotation is "Lunge", then + this value is set to true. + uima.cas.Boolean + + + matchedText + The text in document which matched the synonym (in the respective mapping mode + form, i.e., segment/stem/original etc.). + uima.cas.String + + + matchedTerm + The synonym of the concept which caused the match (in the + ConceptAnnotator-dictionary this is <term label=xxx>). + uima.cas.String + + + matchedVariant + The variant of the synonym of the concept which caused the match (in the + ConceptAnnotator-dictionary this is <variant label=xxx>). + Note that one synonym (matchedTerm) can have several variants (i.e. spelling forms or mapping + forms). + uima.cas.String + + + matchedTokens + The Token annotations on which the concept was found. + Note that there is also matchedAnnotations which list the actual annotations involved in the + matching process (i.e., token, stem, segment, etc.). + uima.cas.FSArray + de.averbis.extraction.types.Token + true + + + matchedAnnotations + List of the actual annotations involved in the matching process (i.e., original, + stem, segment, etc.). + Note that there is also matchedTokens, which lists only matching Token annotations. + uima.cas.FSArray + true + + + mappingMode + The mode used for mapping (e.g., original, stem, segment...). + uima.cas.String + + + mappingFuzzynessScore + The score for the fuzzyness of the mapping (higher scores mean higher fuzzyness, + i.e., less exact mappings). + uima.cas.Float + + + uniqueID + The unique concept id, including terminology name and concept ID + should look like this: <terminologyName>:<conceptID>. + uima.cas.String + + + conceptID + The concept id. For a unique id refer to uniqueID. + uima.cas.String + + + source + The name of the terminology source. + uima.cas.String + + + + + de.averbis.extraction.types.CoreAnnotation + The base type for all annotation types providing a componentId and confidence. + uima.tcas.Annotation + + + componentId + The id/name of the component that created this annotation. + uima.cas.String + + + confidence + Confidence value of the current annotation. E.g. in the case the annotation has + been created by a statistical analysis engine. + uima.cas.Double + + + confidenceKind + Additional information about the specific kind of confidence. This provides an + option to indicate if the confidence feature is set at all. + uima.cas.String + + + + + de.averbis.extraction.types.Descriptor + An index term from an ontology; its type (or reference) is written in the feature + annotation. + de.averbis.extraction.types.IndexTerm + + + uid + The unique identifier of the descriptor, e.g., a combination of terminology and + concept id. + uima.cas.String + + + + + de.averbis.extraction.types.Entity + A named entity; not to be confused with a Concept. A (named) entity is a string + representation in text referring to a class of entities. Thus, the entity mention does not have + an identifier but a specific type (the category) assigned to it. + de.averbis.extraction.types.CoreAnnotation + + + value + This feature provides the text of the annotated mention. Important for easily + representing discontinuous mentions such as 'T cell' in the expression 'T and B cell'. + uima.cas.String + + + label + The type of the entity; e.g., PERSON, LOCATION etc. + Feature name is label due to the fact that "type" is a reserved word. + uima.cas.String + + + parsedElements + Reference to all recognized entities inside this Entity such as Size, Time, Area, + Date, Volume, .... + uima.cas.FSArray + de.averbis.extraction.types.Entity + true + + + + + de.averbis.extraction.types.Enumeration + A specific group representing an enumeration like "red, blue and green". + de.averbis.extraction.types.Group + + + de.averbis.extraction.types.GenericMetadata + Type holding generic metadata information of a document. Multiple annotations should + be used to add additional metadata to the CAS. + de.averbis.extraction.types.CoreAnnotation + + + metadataFieldname + To reduce the potential metadata field names, the predefined field names should be + used where possible (add new field names if necessary). + Predefined metadata field names are: title, summary, filesize, annotatorName. + uima.cas.String + + + value + Value of the metadata field, e.g. + metadataFieldname = title, + value = "Brave new world". + uima.cas.String + + + + + de.averbis.extraction.types.Group + Groups together a set of annotations that belong together, e.g., enumerations. One + of them can be set to the "leading" concept. + E.g. "the liver metastasis is hypodense and has a size of 3cm*2cm". + lead: metastasis, other concepts: liver, hypodense, 3cm*2cm + de.averbis.extraction.types.CoreAnnotation + + + leadingAnnotation + Optional annotation indicating the leading head of hte group. + de.averbis.extraction.types.CoreAnnotation + + + members + Annotations contained in the group. + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + label + Textual label describing the group elements. + uima.cas.String + + + + + de.averbis.extraction.types.Header + The header annotation of a document + de.averbis.extraction.types.CoreAnnotation + + + docID + The ID of the document. + uima.cas.String + + + source + The source of the document. + uima.cas.String + + + path + The path of the document. + uima.cas.String + + + fileName + The name of the source file (often used by cas consumers which produce an output + file for each CAS; this name is used as base). + uima.cas.String + + + fileEncoding + The encoding of the file. + uima.cas.String + + + documentIndex + The current number of the documents, i.e. a document is number 5 in a complete + sequence. + uima.cas.Integer + + + lastFile + Indicates if this is the last file. + uima.cas.Boolean + + + sourceLanguage + The document language of the source. + uima.cas.String + + + offsetInSource + Byte offset of the start of document content within original source file or other + input source. Only used if the CAS document was retrieved from an source where one physical + source file contained several conceptual documents. Zero otherwise. + uima.cas.Integer + + + documentSize + Size of original document in bytes before processing by CAS Initializer. Either + absolute file size of size within file or other source. + uima.cas.Integer + + + sequenceNumber + Sequence number to test the right order while merging CASes. + uima.cas.Integer + + + lastSegment + For a CAS that represents a segment of a larger source document, this flag + indicates whether this CAS is the final segment of the source document. This is useful for + downstream components that want to take some action after having seen all of the segments of a + particular source document. + uima.cas.Boolean + + + + + de.averbis.extraction.types.IndexTerm + A term to be used for indexing a document. + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the index term. Example: the normalized and stemmed + string which represents a keyword in the free keywording scenario or for controlled keywording + (=descriptor extraction) the dictCanon might be written here. + uima.cas.String + + + baseAnnotation + The annotation to be assigned as index term. This can i.e. be a Concept or a Noun + Phrase annotation from which the index term was derived. + de.averbis.extraction.types.CoreAnnotation + + + + + de.averbis.extraction.types.InputParam + InputParam is used to pass parameters to an analysis engine via a JCas object. This + may be used to pass parameters + in the process() method of an analysis engine rather than during initialization of the AEs. It is + e.g. necessary + for the ConceptAnnotator at which you want to pass restrictions (such as "language" or + "terminology") for each single + text/jcas while only having one ConceptAnnotator instance. + de.averbis.extraction.types.CoreAnnotation + + + key + The key of the input parameter. + uima.cas.String + + + values + The values of the input parameter. + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Keyword + A keyword that is assigned freely (i.e., not taken from an ontology) to a document. + Its type is written in the feature annotation + de.averbis.extraction.types.IndexTerm + + + de.averbis.extraction.types.Lemma + Lemma is the canonical form of a lexeme. Lemmata can be retrieved from lexicon or be + produced by lemmatizer. + de.averbis.extraction.types.CoreAnnotation + + + value + The value of the lemma. + uima.cas.String + + + case + Case such as Nom (Nominative) or Gen (Genitive) etc. + uima.cas.String + + + number + Singular or plural. + uima.cas.String + + + gender + fem or masc or neutr. + uima.cas.String + + + + + de.averbis.extraction.types.Listing + A specific group representing a listing like "1. red 2. blue 3. green". + de.averbis.extraction.types.Group + + + de.averbis.extraction.types.Member + Utility annotation for indicating a member of a group. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.extraction.types.POSTag + Parent type for all specific part-of-speech types. + de.averbis.extraction.types.CoreAnnotation + + + tagsetId + The name of the tag set the pos tag belongs to; e.g. the "Penn Treebank II Tags" + (see http://bulba.sdsu.edu/jeanette/thesis/PennTags.html) + uima.cas.String + + + value + The specific part-of-speech tag, as returned by the POS-Tagger (e.g., "NN" or + "ADJ" etc) + uima.cas.String + + + + + de.averbis.extraction.types.POSTagAdj + The type for all POS-Tags of the type "Adjective". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagAdp + The type for all POS-Tags of the type "Preposition/Postposition". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagAdv + The type for all POS-Tags of the type "Adverb". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagConj + The type for all POS-Tags of the type "Conjunction". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagDet + The type for all POS-Tags of the type "Determiner". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagNoun + The type for all POS-Tags of the type "Noun". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagNum + The type for all POS-Tags of the type "Numeral". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPart + The type for all POS-Tags of the type "Particle". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPron + The type for all POS-Tags of the type "Pronoun". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPunct + The type for all POS-Tags of the type "Punctuation". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagVerb + The type for all POS-Tags of the type "Verb". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.Paragraph + Different paragraphs found in the document. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Relation + Describes a binary relation between two annotations. + The relation is defined according to the SPO (subject, predicate, object) annotation. + de.averbis.extraction.types.CoreAnnotation + + + subject + An annotation representing the subject of the relation ("agens"). + de.averbis.extraction.types.CoreAnnotation + + + predicate + The annotation representing the predicate of the relation + e.g. + BASF has integrated BAYER + --> 'has integrated' is the predicate that is marked as ChunkVP + --> use the feature 'value' to define the type of the relation + --> value: acquisition + de.averbis.extraction.types.CoreAnnotation + + + object + The object of the relation. + de.averbis.extraction.types.CoreAnnotation + + + value + Type of the relation. + uima.cas.String + + + + + de.averbis.extraction.types.ResolvedEntity + A special entity with an additional specific resolved form. + de.averbis.extraction.types.Entity + + + resolvedType + The type of the resolved form. + uima.cas.String + + + resolvedForm + A string representing the resolved form of the entity. + uima.cas.String + + + + + de.averbis.extraction.types.Section + Text sections of a certain type. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Segment + The segmentation of a text part; a segment is usually a subword (i.e., part of a + token). + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the segment. + uima.cas.String + + + isValidSegmentation + Indicates if the segmentation is valid (viz. could be completely matched against + the dictionary). + uima.cas.Boolean + + + midStrings + The MID value, multiple for ambiguous MIDs (for MID see Morphosaurus Paper). + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Sentence + Annotation representing a sentence including the ending punctuation mark. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.extraction.types.Stem + The type for stem annotations. + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the stem. + uima.cas.String + + + + + de.averbis.extraction.types.SummarySentence + Annotation indicating a sentence that makes up a summary of the document. + de.averbis.extraction.types.CoreAnnotation + + + sentence + The sentence annotation that contains the content of this summary sentence. + de.averbis.extraction.types.Sentence + + + descriptors + The descriptors extracted by the algorithm accounting to the selection of the + sentence. + uima.cas.FSArray + de.averbis.extraction.types.Descriptor + true + + + + + de.averbis.extraction.types.Title + Marks a title in the document. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Token + Annotation for basic textual units including word, numbers and punctuation marks. + de.averbis.extraction.types.CoreAnnotation + + + posTag + The part of speech of this token (i.a. used for concept annotator to be restricted + to certain pos types). + de.averbis.extraction.types.POSTag + + + segments + Segments of this token (i.a. used for respective mode in concept annotator). + uima.cas.FSArray + de.averbis.extraction.types.Segment + true + + + stem + The stem of the token (i.a. used for respective mode in concept annotator). + de.averbis.extraction.types.Stem + + + isAbbreviation + Marker whether the token is (part of) an abbreviation. + uima.cas.Boolean + + + abbreviations + The abbreviations for the token; this may be used as replacement in concept + annotator. Note, that this goes in combination with "isAbbreviation" marking whether the token + is an abbreviation. + Multiple entries mean that there is ambiguity which full form is correct. There will be components to + resolve this ambiguity which then remove wrong forms. + Components which cannot do this ambiguity resolution must rely that the first (and hopefully only) entry + is correct! + uima.cas.FSArray + de.averbis.extraction.types.Abbreviation + true + + + ignoreByConceptMapper + If this feature is true then the ConceptAnnotator + ignores the token. Use this is a pre-processing + component has already identified the semantic of + the token. E.g. dates, times, measurement values. + Default value: false + uima.cas.Boolean + + + normalized + Normalized version of this token (usually lower-case, without special characters + and number). + uima.cas.String + + + diacriticsFreeVersions + In the case that the normalized version contains diacritics, multiple versions + without diacritics are stored in this array. + uima.cas.StringArray + true + + + isStopword + Indicates if the token is a stopword. + uima.cas.Boolean + + + lemma + The Lemma of the token. + de.averbis.extraction.types.Lemma + + + isInvariant + Defines whether a token is an invariant. Such a token should not undergo some + morphologic analysis steps, such as stemming and/or decompounding. + However, lemmatization might still be allowed. + Typical invariants: IL-2 (gene name) or also product names or numbers (SR-2715) but also too short + words (au). + uima.cas.Boolean + + + tokenClass + The optional string representing the class of the token concerning its surface + form. + uima.cas.String + + + + + de.averbis.extraction.types.ValidTextSegment + Zone to mark valid text in contrast to invalid text which e.g. may be OCR (Optical + Character Recognition) artefacts, number blocks, tables etc. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Zone + An annotation concerning the document structure, e.g. header, title, abstract, etc. + de.averbis.extraction.types.CoreAnnotation + + + label + Allows to annotated the Zone with a semantic label. + E.g. in the case of a section the value might be + Introduction, Appendix,... + uima.cas.String + + + weight + The relevance or weight for a zone; used e.g. to weight information contained in + the respective zone. + uima.cas.Float + + + + + de.averbis.textanalysis.types.AbstractName + The name of a person. + de.averbis.extraction.types.Entity + + + reference + Textual reference of the name. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.AnnotationClassification + General classification result on annotation level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.AnnotationScope + Scope of a cue annotation. + de.averbis.extraction.types.CoreAnnotation + + + label + Optional label indicating the kind of scope. + uima.cas.String + + + cue + The cue indicating the scope. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.ConceptEmbedding + Represents a concept embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.DocumentClassification + General classification result on document level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.DocumentEmbedding + Represents a document embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.Embedding + Represents an embedding for a given target annotation. + de.averbis.extraction.types.CoreAnnotation + + + vector + The actual dense embedding vector. + uima.cas.DoubleArray + true + + + dimension + The dimension of the embedding. + uima.cas.Integer + + + kind + The kind of the embedding. + uima.cas.String + + + id + Identifier representing the embedding model. + uima.cas.String + + + reference + The original annotation represented by the embedding. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.FirstName + The first name. + de.averbis.textanalysis.types.AbstractName + + + de.averbis.textanalysis.types.GenericClassification + A classification result. + de.averbis.extraction.types.CoreAnnotation + + + group + Group indicating the classification context. + uima.cas.String + + + label + Label indicating the classification result. + uima.cas.String + + + annotation + Optional reference to the classified annotation or category. + uima.tcas.Annotation + + + featureImpacts + Optional information concerning the weight/importance/impact of specific features. + uima.cas.StringArray + true + + + relevantSpans + Optional information concerning the position of relevant spans. + uima.cas.FSArray + de.averbis.textanalysis.types.PredictionRelevantSpan + true + + + + + de.averbis.textanalysis.types.GenericCue + A generic cue. + de.averbis.extraction.types.CoreAnnotation + + + label + Optional label indicating the kind of cue. + uima.cas.String + + + + + de.averbis.textanalysis.types.LastName + The last name. + de.averbis.textanalysis.types.AbstractName + + + de.averbis.textanalysis.types.ParagraphEmbedding + Represents a paragraph embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.PersonName + The name of a person. + de.averbis.textanalysis.types.AbstractName + + + firstName + Person's first name. + de.averbis.textanalysis.types.FirstName + + + lastName + Person's last name. + de.averbis.textanalysis.types.LastName + + + + + de.averbis.textanalysis.types.PredictionRelevantSpan + A span pointing to relevant annotations for a specific classification. + de.averbis.extraction.types.CoreAnnotation + + + relatedAnnotations + Relevant source annotations. + uima.cas.FSArray + uima.tcas.Annotation + true + + + featureImpacts + Relevant features for identifying this span. + uima.cas.StringArray + true + + + + + de.averbis.textanalysis.types.RelationClassification + General classification result on annotation relation level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.SentenceEmbedding + Represents a sentence embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.WordEmbedding + Represents a word embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.Wordpiece + A tokenized part of a word. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized (and lowercased) version of the wordpiece without accents. + uima.cas.String + + + embedding + Optional embedding of this wordpiece. + de.averbis.textanalysis.types.WordpieceEmbedding + + + tokenStart + Flag indicating that the word piece is located at the beginning of a token. + uima.cas.Boolean + + + tokenStartWordpiece + Optional reference to additional wordpiece representing the start of a token. + de.averbis.textanalysis.types.Wordpiece + + + vocabularyIndex + Index of wordpiece in the vocabulary. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.WordpieceEmbedding + Represents a wordpiece embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + tokenStartEmbedding + Optional embedding of an additional token start wordpiece. + de.averbis.textanalysis.types.WordpieceEmbedding + + + + + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + Parent type for all evaluation types which is able to store a reference annotation. + de.averbis.extraction.types.CoreAnnotation + + + annotation + The corresponding annotation. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.evaluation.FalseNegative + An annotation was not found but should have been found. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.FalsePositive + An annotation was found but should not have been found. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.PartialPositive + A partially correct annotation. + de.averbis.textanalysis.types.evaluation.TruePositive + + + de.averbis.textanalysis.types.evaluation.SimilarityMatching + Various information of candidate matches for debugging purposes. + de.averbis.extraction.types.CoreAnnotation + + + candidate + The corresponding annotation. + uima.tcas.Annotation + + + predicted + All predicted labels for candidate. + uima.cas.StringArray + true + + + + + de.averbis.textanalysis.types.evaluation.TrueNegative + A correctly missing annotation. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.TruePositive + A correct annotation. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.health.Abnormal + Abnormal observation. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + de.averbis.textanalysis.types.health.AbstractDrug + Supertype of the drugs. + de.averbis.extraction.types.CoreAnnotation + + + brandName + The brand name of the drug. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.AbstractInterpretation + Abstract supertype for interpretations. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AbstractObservation + Abstract type for observations, like laboratory values, vital signs, etc. + de.averbis.extraction.types.CoreAnnotation + + + parameter + The actual parameter of the observation. + de.averbis.extraction.types.Concept + + + date + The date of the observation. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + Abstract type for lymph node mentions. + de.averbis.textanalysis.types.health.TNMBasic + + + attacked + Number of attacked lymph nodes. + uima.cas.Integer + + + tested + Number of tested lymph nodes. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.AdditionalDoseAmount + Textspan specifying additional information of the dose amount. + de.averbis.extraction.types.CoreAnnotation + + + value + The numeric value describing the additional amount. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.AdditionalDoseAmountIndicator + Indicator for following additional dose amount. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Administration + Textspan specifying a route of administration. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AdmissionDateInd + Indicator for a following admission date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AdmissionDiagnosisSection + Section containing information about diagnosis on admission. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AdmissionMedicationSection + Admission can refer to hospital admission, long-term care admission, or home health admission. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.AdmissionReasonSection + This section records the patient's reason for their visit (the provider's description of the reason + for visit). Local policy determines whether the information is divided into two sections or recorded + in one section serving both purposes. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AdverseEventSection + Contains a list and description of any allergies or adverse reactions pertinent to current or past + medical history. At a minimum this section should contain currently active and any relevant historical + allergies and adverse reactions. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AnamnesisSection + History general describes all aspects of medical history of the patient even if not pertinent to the + current procedure, and may include chief complaint, past medical history, social history, family + history, surgical or procedure history, medication history, and other history information. + The history may be limited to information pertinent to the current procedure or may be more + comprehensive. It may also be reported as a collection of random clinical statements or it may be + reported categorically. Categorical report formats may be divided into multiple subsections, including + Past Medical History and Social History. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.AngiogramSection + Section containing information about angiogram. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.AnteriorEyeSegmentSection + Section containing information about the anterior eye segment. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.BiologicalProductConcept + Concept type for the material of a biologically derived product. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.BiologicallyDerivedProduct + A material substance originating from a biological entity intended + to be transplanted or infused into another (possibly the same) biological entity. + Example: hematopoietic stem cells. + de.averbis.extraction.types.CoreAnnotation + + + product + The material concept of the product. + de.averbis.extraction.types.Concept + + + quantity + The quantity of the biologically derived product. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + time + Date or time of the transplantation. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.health.BiopsyIndicator + Indicators that document contains biopsy report. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BirthDateIndicator + Indicator for a following birth date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BloodPressure + Annotation for blood pressure. + de.averbis.textanalysis.types.health.AbstractObservation + + + systolic + Measurement of systolic blood pressure. + de.averbis.textanalysis.types.measurement.Measurement + + + diastolic + Measurement of diastolic blood pressure. + de.averbis.textanalysis.types.measurement.Measurement + + + interpretation + Interpretation of fact depending on reference values or interpretation in text. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + + + de.averbis.textanalysis.types.health.BloodPressureConcept + Concept type for blood pressure. + de.averbis.textanalysis.types.health.VitalSignConcept + + + de.averbis.textanalysis.types.health.BloodPressureIgnore + Ignore patterns for blood pressure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BooleanQualitativeValue + Supertype for qualitative values with boolean result. + de.averbis.textanalysis.types.health.QualitativeValue + + + de.averbis.textanalysis.types.health.BreastQuadrant + Aggregating annotation for breast quadrants storing additional information. + de.averbis.extraction.types.CoreAnnotation + + + clock + The location given by a clock value. + de.averbis.textanalysis.types.health.LocationClock + + + side + The side of the quadrant. + de.averbis.textanalysis.types.health.LocationSide + + + horizontal + The horizontal orientation. + de.averbis.textanalysis.types.health.LocationHorizontal + + + vertical + The vertical orientation. + de.averbis.textanalysis.types.health.LocationVertical + + + + + de.averbis.textanalysis.types.health.BreastTopographyConcept + The concept type for topography concepts describing a part of breast. + de.averbis.textanalysis.types.health.TopographyConcept + + + concept + The referenced source concept. + de.averbis.extraction.types.Concept + + + quadrant + The referenced source quadrant. + de.averbis.textanalysis.types.health.BreastQuadrant + + + + + de.averbis.textanalysis.types.health.Candidate + Supertype for candidate annotations of a diagnosis, procedure etc. + de.averbis.extraction.types.CoreAnnotation + + + conceptID + The id of the candidate. + uima.cas.String + + + dictCanon + An optional preferred term corresponding to the given id. + uima.cas.String + + + matchedTerm + Additional information about the match. + uima.cas.String + + + approach + The approach that generated this candidate. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Chimerism + Annotation for chimerism. + de.averbis.extraction.types.CoreAnnotation + + + kind + The kind of the actual chimerism: COMPLETE or MIXED. + uima.cas.String + + + value + Numeric value of chimerism. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + date + Date of chimerism analysis. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.ChimerismIndicator + Annotation for chimerism indicators. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ClinicalSection + Section type for clinical sections. + de.averbis.extraction.types.Section + + + concept + Concept indicating actual section. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + headline + Headline annotation of actual section. + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + + + content + Content annotation of actual section. + de.averbis.textanalysis.types.health.ClinicalSectionContent + + + + + de.averbis.textanalysis.types.health.ClinicalSectionCandidate + Candidates of clinical sections. + de.averbis.extraction.types.CoreAnnotation + + + headline + Headline of actual clinical section candidate. + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + + + content + Content of actual clinical section candidate. + de.averbis.textanalysis.types.health.ClinicalSectionContent + + + + + de.averbis.textanalysis.types.health.ClinicalSectionCandidateWithoutHeadline + Candidates of clinical sections without headline. + de.averbis.textanalysis.types.health.ClinicalSectionCandidate + + + concept + Non headline concept indicating actual section. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + + + de.averbis.textanalysis.types.health.ClinicalSectionContent + Clinical section content. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + Clinical section headline. + de.averbis.extraction.types.CoreAnnotation + + + headlineConcept + Concept annotation indicating headline. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + + + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + Concept type for clinical section keywords. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.ClinicalStatusIndicator + Indicator for a clinical status of a diagnosis. Interpretation could be e.g. ACTIVE, RESOLVED etc. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.ConceptClassification + A classification for concept annotations. + de.averbis.extraction.types.CoreAnnotation + + + label + The category of the annotation, e.g., final. + uima.cas.String + + + concept + The category of the annotation, e.g., final. + de.averbis.extraction.types.Concept + + + + + de.averbis.textanalysis.types.health.ConditioningTreatmentSection + Myeloablative conditioning treatment such as irradiation therapy or chemotherapy. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.DayTimeDoseFrequency + Details of dose frequency for a specific time of day. + de.averbis.textanalysis.types.health.DoseFrequency + + + morning + Number of drug units in the morning. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + midday + Number of drug units at midday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + evening + Number of drug units in the evening. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + atNight + Number of drug units at night or bedtime. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.DeathDate + Recorded date of patient's death. + de.averbis.extraction.types.CoreAnnotation + + + date + Patient's date of death. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.Diagnosis + The actual diagnosis containing the concept and additional information. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + laterality + The laterality of the actual diagnosis. + de.averbis.textanalysis.types.health.Laterality + + + belongsTo + Diagnosis of patient or other person (family anamnesis). Possible values include 'patient' or 'family'. + uima.cas.String + + + onsetDate + The onset date of the diagnosis. + de.averbis.textanalysis.types.temporal.Date + + + kind + The kind of the diagnosis. Possible values include 'main' or 'secondary'. + uima.cas.String + + + clinicalStatus + Clinical status of the actual diagnosis. + de.averbis.textanalysis.types.health.Status + + + verificationStatus + Verification status of the actual diagnosis. Possible values: "NEGATED" if Concept is negated. + de.averbis.textanalysis.types.health.Status + + + approach + The approach that generated this diagnosis annotation. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.DiagnosisCandidate + A diagnosis candidate for a DRG coding. + de.averbis.textanalysis.types.health.Candidate + + + belongsTo + Diagnosis candidate belongs to patient or other person (family anamnesis). Possible values include 'patient' or 'family'. + uima.cas.String + + + clinicalStatus + Clinical status of the diagnosis candidate. + de.averbis.textanalysis.types.health.Status + + + verificationStatus + Verification status of the diagnosis candidate. + de.averbis.textanalysis.types.health.Status + + + + + de.averbis.textanalysis.types.health.DiagnosisCodeConcept + Concept type for diagnoses given by their code. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.DiagnosisConcept + Concept type for diagnoses. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DiagnosisConceptCandidate + A text span that might contain a DiagnosisConcept. + de.averbis.extraction.types.CoreAnnotation + + + additionalSpans + Optional annotation not in the initial span, which can influence the coding. + uima.cas.FSArray + true + + + fragments + List of annotations in span excluding the undesired indicators (e.g. LateralityIndicator) . + uima.cas.FSArray + true + + + + + de.averbis.textanalysis.types.health.DiagnosisHistorySection + History of past illness describes the history related to their current complaints, problems, + or diagnoses. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.DiagnosisSection + History of present illness describes the history related to the reason for a given procedure. It + contains the historical details leading up to and pertaining to the patient's current complaint or + reason for seeking medical care. Because history of present illness can include past surgical history + and other procedures, the Procedure History section may be included under the History of Present + Illness section or it may stand alone as its own section. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.DiagnosisSpecialConcept + Special induced Concept type for diagnoses. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.DiagnosisStatus + Clinical status (active, resolved) or verification status (assured, negated, unknown, ...) of a diagnosis. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.DischargeDateInd + Indicator for a following discharge date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.DischargeDiagnosisSection + Hospital discharge diagnosis describes the patient's relevant problems or diagnoses that occurred + during the hospitalization or that need to be followed after hospitalization. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.DischargeFindingSection + Hospital discharge physical findings records a narrative description of the patient's physical findings. + de.averbis.textanalysis.types.health.FindingSection + + + de.averbis.textanalysis.types.health.DischargeMedicationSection + Hospital discharge medications defines the medications that the patient is intended to take (or stop) after + discharge. This may also include a patient's prescription history and indicate the source of the medication + list, for example, from a pharmacy system versus from the patient. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.DocumentFooterSection + Section containing document footer. + de.averbis.textanalysis.types.health.MiscClinicalSection + + + de.averbis.textanalysis.types.health.DoseFormConcept + Concept type for dose forms. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DoseFrequency + Supertype of the dose frequencies. + de.averbis.extraction.types.CoreAnnotation + + + interval + The taking interval of a medication, e.g. day, week, month etc. + uima.cas.String + + + totalCount + Total count of taken drug units per interval. + uima.cas.Double + + + totalDose + Total dose of taken drug per interval. + de.averbis.textanalysis.types.measurement.Measurement + + + regimen + Annotation of the mentioned regimen, e.g. 'three times daily' + uima.tcas.Annotation + + + concept + Optional concept that was the origin of the dose frequency. + de.averbis.extraction.types.Concept + + + + + de.averbis.textanalysis.types.health.DoseFrequencyConcept + Concept type for dose frequencies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DoseKindIndicator + Utility type for representing specific Dose Kinds, i.e, fractional. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized kind. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Drug + Drug with only one ingredient. + de.averbis.textanalysis.types.health.AbstractDrug + + + ingredient + The ingredient concept of the actual drug. + de.averbis.textanalysis.types.health.IngredientConcept + + + strength + Strength of the drug + de.averbis.textanalysis.types.health.Strength + + + + + de.averbis.textanalysis.types.health.ECGSection + Section containing information about ECG. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.ECOG + Annotation for ECOG. + de.averbis.textanalysis.types.health.ObservationWithStage + + + de.averbis.textanalysis.types.health.ECOGConcept + Concept type for ECOG. + de.averbis.textanalysis.types.health.StageObservationConcept + + + de.averbis.textanalysis.types.health.EchocardiographySection + Section containing information about echocardiography. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.EpicrisisSection + An evaluation (also called asessment, impression or diagnoses) note represents the clinician's + conclusions and working assumptions that will guide treatment of the patient. The assessment + formulates a specific plan or set of recommendations. The assessment may be a list of specific + disease entities or a narrative block. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.EstrogenReceptor + A estrogen receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.ExtendedNumericValue + + de.averbis.textanalysis.types.numericvalue.NumericValue + + + extendedStringValue + + uima.cas.String + + + + + de.averbis.textanalysis.types.health.EyeIndicator + Indicator for eye mentioning. + de.averbis.textanalysis.types.health.LateralityIndicator + + + de.averbis.textanalysis.types.health.FamilyAnamnesisSection + History of family member diseases is a report of health information, including medical, genetic, + environmental, and lifestyle factors, pertaining to the patient and his or her genetic relatives + (living or deceased). The family history information is used to determine possible or relevant health + risk factors that may have a potential impact on the patient's healthcare risk profile. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.FamilyIndicator + Indicator for a diagnosis in the family. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.FemaleGenderIndicator + Indicator for female gender mentioning. + de.averbis.textanalysis.types.health.GenderIndicator + + + de.averbis.textanalysis.types.health.FindingSection + Section containing information about findings. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.FunctionalAngiographySection + Section containing information about the functional angiography. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.FunctionalStatusSection + Functional status assessment describes the patient's status of normal functioning at the time a care + record was created. Functional statuses include information regarding the patient relative to + ambulatory ability, mental status or competency, activities of daily living (ADLs) (i.e. bathing, + dressing, feeding, grooming), home/living situation having an effect on the health status of the + patient, ability to care for self, social activity (i.e. issues with social cognition, participation + with friends and acquaintances other than family members), occupation activity (i.e. activities partly + or directly related to working), housework or volunteering, family and home responsibilities or + activities related to home and family, communication ability (i.e. issues with speech, writing or + cognition required for communication), and perception, including sight, hearing, taste, skin sensation, + kinesthetic sense, proprioception, or balance. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.GenderIndicator + Indicator for gender mentioning. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.GeneralConditionSection + Physical findings (of general status) describes general observations and readily observable attributes + of the patient, including affect and demeanor, apparent age compared to actual age, gender, ethnicity, + nutritional status based on appearance, body build and habitus (e.g., muscular, cachectic, obese), + developmental or other deformities, gait and mobility, personal hygiene, evidence of distress, and + voice quality and speech. + de.averbis.textanalysis.types.health.FindingSection + + + de.averbis.textanalysis.types.health.GleasonScore + The Gleason score. + de.averbis.extraction.types.CoreAnnotation + + + score + The combined score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + primary + The primary score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + secondary + The secondary score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.GvHD + Annotation of a Graft-versus-Host-Disease diagnosis. + de.averbis.textanalysis.types.health.Diagnosis + + + continuanceStatus + GvHD status, i.e. acute, chronic. + de.averbis.textanalysis.types.health.GvHDContinuanceStatus + + + grade + Grade of the GvHD diagnosis, i.e. I, II, III, IV. + de.averbis.textanalysis.types.health.GvHDGrade + + + stage + Stage of the GvHD diagnosis, i.e. 1, 2, 3, 4 or limited, extensive. + de.averbis.textanalysis.types.health.GvHDStage + + + organ + Organ diagnosed with GvHD, i.e. skin, liver. + de.averbis.textanalysis.types.health.GvHDOrgan + + + date + The date of the diagnosis. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.GvHDContinuanceStatus + (Temporal) Status of the GvHD diagnosis, i.e. acute, chronic. + de.averbis.textanalysis.types.health.DiagnosisStatus + + + de.averbis.textanalysis.types.health.GvHDDiagnosisConcept + Concept type for Graft-versus-Host-Disease diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.GvHDGrade + Severity grade of the GvHD diagnosis, i.e. I, II, III, IV, limited, extended. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized value of GvHD in categories, i.e. I, II, III, IV, limited, extended. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.GvHDOrgan + Organ diagnosed with GvHD, i.e. skin, liver. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized name of affected organ. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.GvHDStage + Stage of the GvHD, i.e. 1, 2, 3, 4. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Stage of GvHD in integer categories, i.e. 1, 2, 3, 4. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.HER2 + A HER2 receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.HLA + Annotation type for human leukocyte antigen. + de.averbis.textanalysis.types.health.AbstractObservation + + + male + Paternal HLA manifestation. + de.averbis.textanalysis.types.health.HLAValue + + + female + Maternal HLA manifestation. + de.averbis.textanalysis.types.health.HLAValue + + + samplingDate + Date of sampling. + de.averbis.textanalysis.types.temporal.Date + + + receiptDate + Date of receipt of sample. + de.averbis.textanalysis.types.temporal.Date + + + belongsTo + Role of the person engaged in a HLA-typed human primary cells transplantation procedure. Possible values are 'RECIPIENT' or 'DONOR'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.HLAConcept + HLA parameter concept. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.HLAValue + Manifestation of allele group, HLA-protein etc. in human leukocyte antigen. + de.averbis.extraction.types.CoreAnnotation + + + alleleGroup + Allele group of actual HLA. + uima.cas.String + + + protein + Specific protein of actual HLA. + uima.cas.String + + + synonymousDNA + Synonymous DNA substitution within the coding region. + uima.cas.String + + + noncodingRegionVariant + Differences in non-coding region. + uima.cas.String + + + expressionNote + Suffix to code changes in expression. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.High + Observation higher than normal. + de.averbis.textanalysis.types.health.Abnormal + + + de.averbis.textanalysis.types.health.Hospitalisation + Hospitalisation of a patient. + de.averbis.extraction.types.CoreAnnotation + + + admissionDate + Date of admission to hospital. + de.averbis.textanalysis.types.temporal.Date + + + dischargeDate + Date of discharge from hospital. + de.averbis.textanalysis.types.temporal.Date + + + duration + Duration of stay in hospital. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.HospitalisationInd + Indicator for hospitalisation mentioning. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.IgnorePhrase + Ignore type for all kinds of medical annotations. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.IngredientConcept + Concept type for ingredients. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Irradiation + The irradiation therapy (incl. dose, kind and temporal interval). + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the irradiation. + de.averbis.textanalysis.types.health.IrradiationTherapyConcept + + + irradiationDose + The irradiation dose. + de.averbis.textanalysis.types.health.IrradiationDose + + + dateInterval + The temporal interval of the irradiation therapy. + de.averbis.textanalysis.types.temporal.DateInterval + + + + + de.averbis.textanalysis.types.health.IrradiationDose + The irradiation dose along with its distribution kind. + de.averbis.extraction.types.CoreAnnotation + + + dose + The irradiation dose measurement value. + de.averbis.textanalysis.types.measurement.Measurement + + + kind + The type of irradiation, i.e. fractional. + de.averbis.textanalysis.types.health.DoseKindIndicator + + + + + de.averbis.textanalysis.types.health.IrradiationTherapyConcept + Concept type for irradiation therapies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.LabValueIgnore + Helper type for representing text spans that should be ignored by the pattern building LaboratoryValue. + uima.tcas.Annotation + + + de.averbis.textanalysis.types.health.LaboratoryConcept + Laboratory parameter concept. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.LaboratorySection + Section containing laboratory information. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.LaboratoryValue + The actual laboratory value containing the concept and additional information. + de.averbis.textanalysis.types.health.AbstractObservation + + + fact + Measurement or numeric value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + factAssessment + A optional relative assessment of the fact. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + lowerLimit + Lower reference value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + upperLimit + Upper reference value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + interpretation + Interpretation of fact depending on reference values or interpretation in text. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + qualitativeValue + Qualitative value of the actual laboratory value, e.g. positive, negative. + de.averbis.textanalysis.types.health.QualitativeValue + + + belongsTo + Laboratory value belongs to patient or other person. Possible values are 'RECIPIENT', 'DONOR' or 'FAMILY'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LaboratoryValueContext + An indicator annotation specifying that a nearby span is part of a lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Laterality + Laterality of an annotation, e.g. diagnosis or ophthalmology. + de.averbis.extraction.types.CoreAnnotation + + + value + Laterality value, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + reference + Indicator that determines the laterality. + de.averbis.textanalysis.types.health.LateralityIndicator + + + + + de.averbis.textanalysis.types.health.LateralityContext + Context with the same laterality. + de.averbis.extraction.types.CoreAnnotation + + + reference + Laterality of the context. + de.averbis.textanalysis.types.health.Laterality + + + + + de.averbis.textanalysis.types.health.LateralityForCodeIndicator + Indicator for the laterality of an annotation, e.g. diagnosis. Only valid if close to a ICD-10 Code. + de.averbis.extraction.types.CoreAnnotation + + + value + Value the indicator stands for, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LateralityIndicator + Indicator for the laterality of an annotation, e.g. diagnosis or ophthalmology. + de.averbis.extraction.types.CoreAnnotation + + + value + Value the indicator stands for, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LeftEyeIndicator + Indicator for mentioning of left eye. + de.averbis.textanalysis.types.health.EyeIndicator + + + de.averbis.textanalysis.types.health.Limit + Limit value from text or external source. + de.averbis.textanalysis.types.measurement.Measurement + + + externalSource + Information about limit value from external source. + uima.cas.Boolean + + + + + de.averbis.textanalysis.types.health.LocationClock + The position/location given by a clock value. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationHorizontal + The position/location given by a horizontal orientation. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationSide + The location given by the side: R, L, T, U + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationVertical + The position/location given by a vertical orientation. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.Low + Observation lower than normal. + de.averbis.textanalysis.types.health.Abnormal + + + de.averbis.textanalysis.types.health.MainDiagnosisSection + Chief complaint records the patient's primary complaint (the patient's own description). + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.MaleGenderIndicator + Indicator for male gender mentioning. + de.averbis.textanalysis.types.health.GenderIndicator + + + de.averbis.textanalysis.types.health.MedicalNegation + Annotations of medical negations. + de.averbis.extraction.types.CoreAnnotation + + + negating + List of concepts which are negated by current negation. + uima.cas.FSArray + de.averbis.extraction.types.Concept + true + + + + + de.averbis.textanalysis.types.health.MedicalPostNegation + Medical negation which negates precedent concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalPreNegation + Medical negation which negates subsequent concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalPrePostNegation + Medical negation which negates surrounding concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalSegmentNegation + Medical negation which negates self-negating concepts (e.g. tumorfrei). + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.Medication + The actual medication containing the concept and additional information. + de.averbis.extraction.types.CoreAnnotation + + + drug + Drug or multi drug of the actual medication. + de.averbis.textanalysis.types.health.AbstractDrug + + + doseForm + Dose form of the actual medication. + de.averbis.textanalysis.types.health.DoseFormConcept + + + doseFrequency + Dose frequency of the actual medication. Could be AbstractDoseFrequency or DailyDoseFrequency, WeeklyDoseFrequency etc. + de.averbis.textanalysis.types.health.DoseFrequency + + + date + Temporal information about the actual medication. + de.averbis.extraction.types.CoreAnnotation + + + administrations + The routes of administration of this medication. + uima.cas.FSArray + de.averbis.textanalysis.types.health.Administration + true + + + additionalAmounts + Additional mentions of dose amounts, e.g., 2 doses. + uima.cas.FSArray + de.averbis.textanalysis.types.health.AdditionalDoseAmount + true + + + status + Status of the medication, e.g. ADMISSION, DISCHARGE. For all available value see MedicationStatus. + de.averbis.textanalysis.types.health.MedicationStatus + + + termTypes + Additional information on clinical drug, e.g. semantic clinical drug (RxNorm Term Type). + uima.cas.FSArray + de.averbis.textanalysis.types.health.TTY + true + + + atc + The ATC Code of the medication. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.MedicationContext + An indicator annotation specifying that a nearby span is part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationHistorySection + History of medication use defines a patient's current medications and history of pertinent medications. + This term may also include a patient's prescription and dispense history. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.MedicationIgnore + Abstract super type for text spans that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationIgnoreEntity + Text spans based on a given annotation that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationIgnorePhrase + Text spans based on dictionaries or patterns that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationRecommendationSection + Recommendation for medication after discharge. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.MedicationSection + Medications administered defines medications and fluids administered during the procedure, excluding + anesthetic medications. Medications administered for anesthesia are typically documented in the + section on Anesthesia. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.MedicationStatus + Status of the medication. Available values: null, ADMISSION, ALLERGY, INPATIENT, DISCHARGE, NEGATED, CONSIDERED, INTENDED, FAMILY, CONDITIONING_TREATMENT, UNKNOWN. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.MedicationStatusIndicator + Indicator for a status of a medication. Interpretation could be e.g. NEGATED, CONSIDERED, ADMISSION, DISCHARGE. For all available value see MedicationStatus. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.MicroBiologyQualitativeValue + Qualitative values for micro biology laboratory concepts, e.g. 'Bacteria'. + de.averbis.textanalysis.types.health.QualitativeValue + + + de.averbis.textanalysis.types.health.MiscClinicalSection + Section containing other information. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ModifierIndicator + Indicator for modifiers. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized value of the modifier, e.g. 'WEAK'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.MorphologyClassification + A classification for morphology annotations. + de.averbis.textanalysis.types.health.ConceptClassification + + + de.averbis.textanalysis.types.health.MorphologyCodeConcept + The concept type for morphology concepts given by their codes. + de.averbis.textanalysis.types.health.MorphologyConcept + + + de.averbis.textanalysis.types.health.MorphologyConcept + The concept type for all morphology concepts. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.MorphologySpecialConcept + The concept type for morphology concepts mostly induced by some additional logic. + de.averbis.textanalysis.types.health.MorphologyConcept + + + de.averbis.textanalysis.types.health.MultiDrug + Drug with more than one ingredient. + de.averbis.textanalysis.types.health.AbstractDrug + + + drugs + List of all drugs contained in the actual multi drug + uima.cas.FSArray + de.averbis.textanalysis.types.health.Drug + true + + + concept + The original ingredient concept responsible for the multi drug. + de.averbis.textanalysis.types.health.IngredientConcept + + + + + de.averbis.textanalysis.types.health.NYHA + Annotation for NYHA. + de.averbis.textanalysis.types.health.ObservationWithStage + + + de.averbis.textanalysis.types.health.NYHAConcept + Concept type for NYHA. + de.averbis.textanalysis.types.health.StageObservationConcept + + + de.averbis.textanalysis.types.health.NegationScope + The negated scope. + de.averbis.textanalysis.types.AnnotationScope + + + de.averbis.textanalysis.types.health.Negative + Negative result of an observation (no interpretation!). + de.averbis.textanalysis.types.health.BooleanQualitativeValue + + + de.averbis.textanalysis.types.health.NoDiagnosis + An indicator annotation specifying that this span is no part of a diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoDiagnosisContext + An indicator annotation specifying that a nearby span is no part of a diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoDiagnosisContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValue + An indicator annotation specifying that this span is no part of a laboratory value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValueContext + An indicator annotation specifying that a nearby span is no part of a lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValueContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedication + An indicator annotation specifying that this span is no part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedicationContext + An indicator annotation specifying that a nearby span is no part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedicationContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedure + An indicator annotation specifying that this span is no part of a procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedureContext + An indicator annotation specifying that a nearby span is no part of a procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedureContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoQualitativeValue + An indicator annotation specifying that a span is not an qualitative value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Normal + Normal observation. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + de.averbis.textanalysis.types.health.ObservationSection + The Procedure findings section records clinically significant observations confirmed or discovered + during a procedure, treatment or service. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ObservationStage + Stage of the observation, i.e. Stage I, II, 1, 2. + de.averbis.extraction.types.CoreAnnotation + + + normalizedValue + Normalized value of the stage. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.ObservationStageIndicator + Indicator for observation stages, i.e. Stage, status, class etc. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ObservationWithStage + Annotation for observation with stage, i.e. NYHA I, ECOG 3. + de.averbis.textanalysis.types.health.AbstractObservation + + + stage + Observation stage. + de.averbis.textanalysis.types.health.ObservationStage + + + + + de.averbis.textanalysis.types.health.OcularFundusSection + Section containing information about the ocular fundus. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.Ophthalmology + Main type for ophthalmological terms. + de.averbis.textanalysis.types.health.AbstractObservation + + + laterality + Laterality of the ophthalmological term. + de.averbis.textanalysis.types.health.Laterality + + + + + de.averbis.textanalysis.types.health.OphthalmologyConcept + Concept type for ophthalmological terms. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.OphthalmologySection + Section containing information about ophthalmology. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.OpticalCoherenceTomographySection + Section containing information about the optical coherence tomography. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.OrganismConcept + Organism concepts, e.g. Bacteria. + de.averbis.extraction.types.Concept + + + kind + The kind of the OrganismConcept, e.g. 'Bacterium', 'Virus' or 'Fungus' + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Organization + Organization name annotation which stores (optionally) its type and correspondence (e.g. sender, receiver). + de.averbis.extraction.types.CoreAnnotation + + + organizationType + The kind/type of organization (e.g. rehabilitation). + uima.cas.String + + + correspondence + The correspondence type (e.g. sender, receiver). + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PathologyDocumentClassification + A classification for a single pathology document for specific elements and code like + diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + category + The category of the document, e.g., MAMMA. + uima.cas.String + + + diagnosis + The code of the relevant diagnosis. + uima.cas.String + + + topography + The code of the relevant topography. + uima.cas.String + + + morphology + The code of the relevant morphology. + uima.cas.String + + + tumor + The TNM code of the relevant tumor. + uima.cas.String + + + node + The TNM code of the relevant node. + uima.cas.String + + + metastasis + The TNM code of the relevant metastasis. + uima.cas.String + + + grading + The relevant grading. + uima.cas.String + + + location + The relevant location. + uima.cas.String + + + rClass + The relevant R-classification. + uima.cas.String + + + side + The relevant side, e.g., L, R, T. + uima.cas.String + + + lymphnodesAffected + The amount of affected lymph nodes. + uima.cas.Integer + + + lymphnodesTested + The amount of tested lymph nodes. + uima.cas.Integer + + + sentinelLymphnodesAffected + The amount of affected sentinel lymph nodes. + uima.cas.Integer + + + sentinelLymphnodesTested + The amount of tested sentinel lymph nodes. + uima.cas.Integer + + + thickness + The thickness of the skin tumor. + uima.cas.Double + + + lymphaticInvasion + The invasion of the cancer to the lymphatic system. + uima.cas.String + + + vascularInvasion + The invasion of the cancer to the vascular system. + uima.cas.String + + + perineuralInvasion + The invasion of the cancer to the space surrounding a nerve. + uima.cas.String + + + resultDate + The date of the result/findings. + uima.cas.String + + + scores + List of different scores, e.g. GleasonScore. + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + categoryAnnotation + Optional annotation representing the category of the document. + de.averbis.extraction.types.Category + + + diagnosisConcept + Optional annotation representing the relevant diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + topographyConcept + Optional annotation representing the relevant topography. + de.averbis.textanalysis.types.health.TopographyConcept + + + morphologyConcept + Optional annotation representing the relevant morphology. + de.averbis.textanalysis.types.health.MorphologyConcept + + + tumorAnnotation + Optional annotation representing the relevant tumor. + de.averbis.textanalysis.types.health.TNMTumor + + + nodeAnnotation + Optional annotation representing the relevant node. + de.averbis.textanalysis.types.health.TNMNode + + + metastasisAnnotation + Optional annotation representing the relevant metastasis. + de.averbis.textanalysis.types.health.TNMMetastasis + + + gradingAnnotation + Optional annotation representing the relevant grading. + de.averbis.textanalysis.types.health.TNMGrading + + + locationAnnotation + Optional annotation representing the relevant location. + de.averbis.textanalysis.types.health.TNMLocation + + + rClassAnnotation + Optional annotation representing the relevant R-classification. + de.averbis.textanalysis.types.health.TNMRClass + + + sideAnnotation + Optional annotation representing the relevant side. + de.averbis.textanalysis.types.health.LocationSide + + + lymphnodesAnnotation + Optional annotation representing the lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodes + + + sentinelLymphnodesAnnotation + Optional annotation representing the sentinel lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + + + thicknessAnnotation + Optional annotation representing the thickness of the skin tumor. + de.averbis.textanalysis.types.health.LaboratoryValue + + + lymphaticInvasionAnnotation + Optional annotation representing the invasion of the cancer to the lymphatic + system. + de.averbis.textanalysis.types.health.TNMAdditional + + + vascularInvasionAnnotation + Optional annotation representing the invasion of the cancer to the vascular + system. + de.averbis.textanalysis.types.health.TNMAdditional + + + perineuralInvasionAnnotation + Optional annotation representing the invasion of the cancer to the space + surrounding a nerve. + de.averbis.textanalysis.types.health.TNMAdditional + + + resultDateAnnotation + Optional annotation representing the date of the findings/result. + de.averbis.textanalysis.types.health.ResultDate + + + + + de.averbis.textanalysis.types.health.PatientContactIndicator + Indicator for a mentioning of a person not related to the patient. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.PatientGender + The gender of the patient. + de.averbis.extraction.types.CoreAnnotation + + + value + Patient's gender value, i.e. female/male. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PatientGroupIndicator + Indicator for a mentioning of a person in the patient's context. + de.averbis.textanalysis.types.health.PersonGroupIndicator + + + de.averbis.textanalysis.types.health.PatientIndicator + Indicator for a mentioning of the patient. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.PatientInformation + Patient information. + de.averbis.extraction.types.CoreAnnotation + + + deathDate + Patient's date of death. + de.averbis.textanalysis.types.health.DeathDate + + + deceased + Patient deceased. + uima.cas.Boolean + + + gender + Patient's gender. + de.averbis.textanalysis.types.health.PatientGender + + + name + Patient's name. + de.averbis.textanalysis.types.health.PatientName + + + + + de.averbis.textanalysis.types.health.PatientName + The patient's name. + de.averbis.textanalysis.types.PersonName + + + de.averbis.textanalysis.types.health.PatientNameConcept + Concept with the patient's full name. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.PersonGroupIndicator + Indicator for the mentioning of a person. + de.averbis.extraction.types.CoreAnnotation + + + value + Description of the person group, e.g. "FAMILY" or "OTHER" + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PhysicalTherapy + []. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the physical therapy. + de.averbis.textanalysis.types.health.PhysicalTherapyConcept + + + status + The status of the physical therapy. + de.averbis.textanalysis.types.health.PhysicalTherapyStatus + + + + + de.averbis.textanalysis.types.health.PhysicalTherapyConcept + Concept type for physical therapies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.PhysicalTherapyStatus + Status of physical therapies. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.PhysicalTherapyStatusIndicator + Indicator for status of physical therapy. Interpretation could be e.g. NEGATED, HISTORY, or PLANNED. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.Positive + Positive result of an observation (no interpretation!). + de.averbis.textanalysis.types.health.BooleanQualitativeValue + + + de.averbis.textanalysis.types.health.PriorLabValueIndicator + Helper type for representing text spans that indicating a prior LaboratoryValue. + uima.tcas.Annotation + + + de.averbis.textanalysis.types.health.PriorLaboratoryValue + A prior LaboratoryValue. + de.averbis.textanalysis.types.health.LaboratoryValue + + + de.averbis.textanalysis.types.health.Procedure + The procedure annotation. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the procedure. + de.averbis.textanalysis.types.health.ProcedureConcept + + + laterality + Laterality of the procedure, i.e. NULL (default), RIGHT, LEFT, BOTH. + de.averbis.textanalysis.types.health.Laterality + + + status + Procedure status feature, i.e. HISTORY, PLANNED, NEGATED. + de.averbis.textanalysis.types.health.ProcedureStatus + + + date + Temporal information about the actual procedure. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.ProcedureCandidate + A procedure candidate for a OPS coding. + de.averbis.textanalysis.types.health.Candidate + + + de.averbis.textanalysis.types.health.ProcedureConcept + Concept type for procedures. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.ProcedureHistorySection + This section defines all interventional, surgical, diagnostic, or therapeutic procedures or treatments + pertinent to the patient historically and at the time the document is generated. + de.averbis.textanalysis.types.health.ProcedureSection + + + de.averbis.textanalysis.types.health.ProcedureSection + Procedure records the descriptions of the procedure with an extensive narrative and may include + procedure site preparation, pertinent details related to measurements and markings, procedure times, + instrumentation, and vital signs and other monitoring data. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ProcedureStatus + Annotation type for procedure status, i.e. HISTORY, PLANNED, NEGATED. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.ProcedureStatusIndicator + Indicator for status of procedure. Interpretation could be e.g. NEGATED, CANCELED, COMNPLETED or PLANNED. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.ProgesteroneReceptor + A progesterone receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.QuadrantElement + Abstract type for element of a quadrant. + de.averbis.extraction.types.CoreAnnotation + + + kind + Label storing the type of indicator, e.g., VERTICAL or SIDE. + uima.cas.String + + + element + The value of the indicator annotation, e.g., BOTTOM or R + uima.cas.String + + + + + de.averbis.textanalysis.types.health.QualitativeValue + Supertype for qualitative values. + de.averbis.extraction.types.CoreAnnotation + + + value + Value of the qualitative value, e.g. 'UNKNOWN', 'ABNORMAL', 'STAINING', 'POSITIVE', 'NEGATIVE'. + uima.cas.String + + + modifier + Modifier for the qualitative value's value, e.g. 'WEAK', 'MODERATE', 'STRONG'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Receptor + A generic receptor providing a status and percentage. + de.averbis.extraction.types.CoreAnnotation + + + status + The status with an interpretation, e.g., "++"". + de.averbis.textanalysis.types.health.ReceptorStatus + + + percentage + The percentage represented as a measurement. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.ReceptorStatus + The status of a receptor. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.Refraction + + de.averbis.extraction.types.CoreAnnotation + + + sphere + + de.averbis.textanalysis.types.health.VANumericValue + + + cylinder + + de.averbis.textanalysis.types.health.VANumericValue + + + axis + + de.averbis.textanalysis.types.health.VANumericValue + + + + + de.averbis.textanalysis.types.health.RelevantVisualAcuity + Best or actual visual acuity, selected from multiple VisualAcuity- or VisualAcuityValues. + de.averbis.textanalysis.types.health.VisualAcuity + + + de.averbis.textanalysis.types.health.RemovedAnnotation + A reference to the annotation that was removed. + de.averbis.extraction.types.CoreAnnotation + + + removed + Annotation that has been removed. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.health.RemovedDiagnosis + A reference to the diagnosis that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedDiagnosisConcept + A reference to the diagnosis concept that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedLaboratoryValue + A reference to the laboratory value that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedMedication + A reference to the medication that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedObservation + A reference to the observation that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.ResultDate + The date of the result/findings. + de.averbis.extraction.types.CoreAnnotation + + + date + Date annotation holding the normalized value. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.RightEyeIndicator + Indicator for mentioning of right eye. + de.averbis.textanalysis.types.health.EyeIndicator + + + de.averbis.textanalysis.types.health.SocialAnamnesisSection + The Social history section contains data defining the patient's occupational, personal (e.g. lifestyle), + social, and environmental history and health risk factors, as well as administrative data such as + marital status, race, ethnicity and religious affiliation. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.SonographySection + Section containing information about sonography. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.SpecialistDepartment + Specialist department with additional information e.g. about department type. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the specialist department. + de.averbis.textanalysis.types.health.SpecialistDepartmentConcept + + + departmentType + Type of the department, e.g. sender. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.SpecialistDepartmentConcept + Concept type for specialist department. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Specimen + Specimen procedure information type. + de.averbis.extraction.types.CoreAnnotation + + + identifier + Identifier of this specimen. + uima.cas.String + + + diagnosis + The diagnosis of the specimen. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + morphology + The morphology of the specimen. + de.averbis.textanalysis.types.health.MorphologyConcept + + + topography + The topography of the specimen. + de.averbis.textanalysis.types.health.TopographyConcept + + + laterality + Optional laterality. + de.averbis.textanalysis.types.health.Laterality + + + descriptions + Additional descriptions of the specimen. + uima.cas.FSArray + de.averbis.textanalysis.types.health.Specimen + true + + + + + de.averbis.textanalysis.types.health.SpecimenSection + The Procedure specimens taken section records the tissues, objects, or samples taken from the patient + during the procedure including biopsies, aspiration fluid, or other samples sent for pathological + analysis. The narrative may include a description of the specimens. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.StageObservationConcept + Concept type for observation stage. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Status + Supertype for status annotations of a diagnosis, medication etc. + de.averbis.extraction.types.CoreAnnotation + + + interpretation + Interpretation of referenced value. + uima.cas.String + + + statusReference + Reference to annotation that specifies/ verifies status. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.health.StatusIndicator + Indicator for a status of a diagnosis, medication etc.. + de.averbis.extraction.types.CoreAnnotation + + + interpretation + Interpretation of referenced value, e.g. ASSURED, NEGATED, SUSPECTED etc. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Strength + The strength of a drug concerning a medication. + de.averbis.extraction.types.CoreAnnotation + + + concept + An optional concept describing the strength. + de.averbis.textanalysis.types.health.StrengthConcept + + + measurement + The actual strength as a measurement + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.StrengthConcept + Concept type for strengths. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.SymptomSection + The Review of systems section contains a relevant collection of symptoms and functions systematically + gathered by a clinician. It includes symptoms the patient is currently experiencing, some of which + were not elicited during the history of present illness, as well as a potentially large number of + pertinent negatives, for example, symptoms that the patient denied experiencing. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.TNMAdditional + Additional TNM mentions + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMBasic + The basic type of a TNM mention providing a value feature. + de.averbis.extraction.types.CoreAnnotation + + + value + The value of the TNM mention. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TNMCertainty + The C-factor, or certainty factor, reflects the validity of classification according + to the diagnostic methods employed. Its use is optional. The C-factor definitions are: + C1: Evidence from standard diagnostic means (e.g., inspection, palpation, and standard radiography, + intraluminal endoscopy for tumors of certain organs). C2: Evidence obtained by special + diagnostic means (e.g., radiographic imaging in special projections, tomography, computerized + tomography [CT], ultrasonography, lymphography, angiography, scintigraphy, magnetic resonance + imaging [MRI], endoscopy, biopsy, and cytology). C3: Evidence from surgical exploration, + including biopsy and cytology. C4: Evidence of the extent of disease following definitive + surgery and pathological examination of the resected specimen. C5: Evidence from autopsy + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMDocumentClassification + The TNM classification result for a document. + de.averbis.extraction.types.CoreAnnotation + + + tumor + tumor + de.averbis.textanalysis.types.health.TNMTumor + + + node + node + de.averbis.textanalysis.types.health.TNMNode + + + metastasis + metastasis + de.averbis.textanalysis.types.health.TNMMetastasis + + + grading + grading + de.averbis.textanalysis.types.health.TNMGrading + + + location + location + de.averbis.textanalysis.types.health.TNMLocation + + + rClass + rClass + de.averbis.textanalysis.types.health.TNMRClass + + + certainty + certainty + de.averbis.textanalysis.types.health.TNMCertainty + + + lymphaticInvasion + lymphaticInvasion + de.averbis.textanalysis.types.health.TNMLymphaticInvasion + + + vascularInvasion + vascularInvasion + de.averbis.textanalysis.types.health.TNMVascularInvasion + + + perineuralInvasion + perineuralInvasion + de.averbis.textanalysis.types.health.TNMPerineuralInvasion + + + additional + additional + de.averbis.textanalysis.types.health.TNMAdditional + + + + + de.averbis.textanalysis.types.health.TNMElement + Abstract type for a TNM element with modifiers. + de.averbis.textanalysis.types.health.TNMEntity + + + modifiers + The prefix modifiers of the element. + uima.cas.FSArray + de.averbis.textanalysis.types.health.TNMModifier + true + + + postModifier + The postfix modifier of the element. + de.averbis.textanalysis.types.health.TNMPostModifier + + + + + de.averbis.textanalysis.types.health.TNMEntity + Abstract type for a TNM entity providing a label. + de.averbis.textanalysis.types.health.TNMBasic + + + label + Label of the entity describing the type of the entity, e.g., TUMOR or GRADING. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TNMGrading + G (1–4): the grade of the cancer cells (i.e. they are "G1" if they are good + differentiated to normal cells, and "G3" if they appear poorly differentiated); + Low grade = Well-differentiated = Grade 1; + Intermediate grade = Moderately differentiated = Grade 2; + High grade = Poorly differentiated = Grade 3; + Undifferentiated = Anaplastic = Grade 4 + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMLocation + Further specification of the metastasis: Pulmonary (PUL), Bone marrow (MAR), Osseous + (OSS), Pleura (PLE), Hepatic (HEP), + Peritoneum (PER), Brain (BRA), Adrenals (ADR), Lymph nodes (LYM), Skin (SKI), Others (OTH) + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMLymphNodes + Information about the attacked and tested lymph nodes. + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + + + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + Information about the attacked and tested sentinel lymph nodes. + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + + + de.averbis.textanalysis.types.health.TNMLymphaticInvasion + Information about the lymphatic invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TNMMetastasis + M: presence of distant metastasis. Mx: metastasis cannot be evaluated. M0: no + distant metastasis. M1: metastasis to distant organs (beyond regional lymph nodes). + de.averbis.textanalysis.types.health.TNMElement + + + de.averbis.textanalysis.types.health.TNMModifier + A modifier of a TNM element + de.averbis.textanalysis.types.health.TNMBasic + + + de.averbis.textanalysis.types.health.TNMNode + N: degree of spread to regional lymph nodes. Examples: Nx: lymph nodes cannot be + evaluated. N0: tumor cells absent from regional lymph nodes. N1: regional lymph node metastasis + present; (at some sites: tumor spread to closest or small number of regional lymph nodes). N2: + tumor spread to an extent between N1 and N3 (N2 is not used at all sites). N3: tumor spread to + more distant or numerous regional lymph nodes (N3 is not used at all sites). + de.averbis.textanalysis.types.health.TNMElement + + + lymphNodes + The attacked and tested lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodes + + + lymphNodesSentinel + The attacked and tested sentinel lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + + + + + de.averbis.textanalysis.types.health.TNMNotation + The aggregating annotation for TNM annotations. + de.averbis.textanalysis.types.health.TNMBasic + + + tumor + The tumor annotations. + uima.cas.FSArray + true + + + node + The node annotations. + uima.cas.FSArray + true + + + metastasis + The metastasis annotations. + uima.cas.FSArray + true + + + grading + The grading annotations + uima.cas.FSArray + true + + + location + The location annotations + uima.cas.FSArray + true + + + rClass + The R class annotations + uima.cas.FSArray + true + + + certainty + The certainty annotations + uima.cas.FSArray + true + + + additional + The additional annotations + uima.cas.FSArray + true + + + + + de.averbis.textanalysis.types.health.TNMPerineuralInvasion + Information about the perineural invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TNMPostModifier + Postmodifier of an element: a, b, c. Among others subclassification of tumor size, + e.g. T1a: tumor under 0.1cm + de.averbis.textanalysis.types.health.TNMBasic + + + de.averbis.textanalysis.types.health.TNMRClass + Residual Tumor (R) Classification. Rx: Presence of residual tumor cannot be + assessed. R0: No residual tumor. R1: Microscopic residual tumor. R2: Macroscopic residual + tumor + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMTumor + T: size or direct extent of the primary tumor. Examples: Tx: tumor cannot be + evaluated. + Tis: carcinoma in situ. T0: no signs of tumor. T1, T2, T3, T4: size and/or extension of the primary + tumor. + de.averbis.textanalysis.types.health.TNMElement + + + de.averbis.textanalysis.types.health.TNMVascularInvasion + Information about the vascular invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TTY + RxNorm Term Type + de.averbis.extraction.types.CoreAnnotation + + + kind + Kind of term type, e.g. SCD. + uima.cas.String + + + code + Term type code for actual medication. + uima.cas.String + + + description + Term type description for actual medication. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Tensio + Annotation for Tensio. + de.averbis.textanalysis.types.health.AbstractObservation + + + leftEye + Tensio measurement of left eye. + de.averbis.textanalysis.types.measurement.Measurement + + + rightEye + Tensio measurement for right eye. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.TensioConcept + Concept type for tensio. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.TensioSection + Section containing information about the tensio. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.TherapySection + This term was originally created for, though not limited in use to, the HL7 Implementation Guide for + CDA: Progress Note. The Interventions section contains information about the specific interventions + provided during the healthcare visit. Depending on the type of intervention(s) provided (procedural, + education, application of assistive equipment, etc.), the details will vary but may include specification + of frequency, intensity, and duration. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.TimeMeasurementDoseFrequency + Details of dose frequency with interval given by a time measurement like daily or each two weeks. + de.averbis.textanalysis.types.health.DoseFrequency + + + de.averbis.textanalysis.types.health.TopographyClassification + A classification for topography annotations. + de.averbis.textanalysis.types.health.ConceptClassification + + + de.averbis.textanalysis.types.health.TopographyCodeConcept + The concept type for topography concepts given by their code. + de.averbis.textanalysis.types.health.TopographyConcept + + + de.averbis.textanalysis.types.health.TopographyConcept + The concept type for all topography concepts. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.TopographySpecialConcept + The concept type for special topography concepts mostly induced by some additional logic. + de.averbis.textanalysis.types.health.TopographyConcept + + + de.averbis.textanalysis.types.health.TransplantationRoleIndicator + An indicator annotation specifying the role of a person, e.g. recipient/donor. + de.averbis.extraction.types.CoreAnnotation + + + role + The role of a person. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TreatmentRecommendationSection + Plan of care notes (previously defined as "Plan of treatment") contains data that defines pending + orders, interventions, encounters, services, and procedures for the patient. The plan includes + prospective, unfulfilled, or incomplete orders and requests only. The plan may also contain + information about ongoing care of the patient and information regarding goals and clinical reminders. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.TumorStage + Stage information describing a tumor mention. + de.averbis.extraction.types.CoreAnnotation + + + stage + The stage of the tumor. + de.averbis.textanalysis.types.health.TumorStageIndicator + + + modifier + Modifier of the tumor stage. + de.averbis.textanalysis.types.health.TumorStageModifierIndicator + + + + + de.averbis.textanalysis.types.health.TumorStageIndicator + Indicator for a tumor stage representing a numeric value. + de.averbis.extraction.types.CoreAnnotation + + + value + Numeric value of the stage. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.TumorStageModifierIndicator + Indicator for a tumor stage modifier. + de.averbis.extraction.types.CoreAnnotation + + + value + Value of the tumor stage modifier indicator. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VANumericValue + Numeric values in context of visual acuity. + de.averbis.extraction.types.CoreAnnotation + + + value + Numeric value. + uima.cas.Double + + + + + de.averbis.textanalysis.types.health.VerificationStatusIndicator + Indicator for a verification status of a diagnosis. Interpretation could be e.g. ASSURED, NEGATED, SUSPECTED etc. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.VisualAcuity + Complex type of visual acuity observation. + de.averbis.textanalysis.types.health.AbstractObservation + + + leftEye + Left eye's visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityValue + + + rightEye + Right eye's visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityValue + + + + + de.averbis.textanalysis.types.health.VisualAcuityAdditionalInformation + + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalization of kind of comment, e.g. "AR_NOT_POSSIBLE" for "AR nicht moeglich", "DOES_NOT_IMPROVE" for "AR bessert nicht". + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuityConcept + Concept type for visual acuity. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.VisualAcuityCorrection + + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalization of visual acuity correction, e.g. "CC" for cum correctione, "AR" for auto refraction. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuityFact + + de.averbis.textanalysis.types.health.VANumericValue + + + normalizedString + Normalization of visual acuity value, e.g. "NLP" for no light perception, "1/20" for "1/20p". + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuitySection + Section containing information about the visual acuity. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.VisualAcuityValue + Visual acuity of one eye. + de.averbis.extraction.types.CoreAnnotation + + + fact + Value of the visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityFact + + + meter + Visual acuity measured with blackboard. + uima.cas.Boolean + + + correction + Correction during measuring visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityCorrection + + + refraction + The measured refraction. + de.averbis.textanalysis.types.health.Refraction + + + pinHole + Visual acuity measured with pin hole. + uima.cas.Boolean + + + additionalInformation + Kind of comment, e.g. "AR_NOT_POSSIBLE", "DOES_NOT_IMPROVE". + de.averbis.textanalysis.types.health.VisualAcuityAdditionalInformation + + + + + de.averbis.textanalysis.types.health.VitalSignConcept + Concept type for vital sign. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.VitalSignSection + Section containing information about vital signs. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.WeekDayDoseFrequency + Details of dose frequency for a specific weekday. + de.averbis.textanalysis.types.health.DoseFrequency + + + monday + Number of drug units on monday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + tuesday + Number of drug units on tuesday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + wednesday + Number of drug units on wednesday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + thursday + Number of drug units on thursday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + friday + Number of drug units on friday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + saturday + Number of drug units on saturday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + sunday + Number of drug units on sunday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.measurement.ComparisonIndicator + A textual representation of a comparison like '<=' or 'unter', also able to + indicate an interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.DictionaryMeasurementMention + A textual representation indicating a measurement. This is a helper type for + measurements that combine numeric values and units or cause other problems for the unit parsing. + de.averbis.extraction.types.CoreAnnotation + + + value + Parseable value of the measurement. + uima.cas.String + + + unit + Parseable unit of the measurement. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.GreaterIndicator + A textual representation indicating something is 'greater', also able to indicate an + interval. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + de.averbis.textanalysis.types.measurement.IntervalIndicator + A textual representation indicating something an interval like '-' or 'bis' + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.LessIndicator + A textual representation indicating something is 'less', also able to indicate an + interval. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + de.averbis.textanalysis.types.measurement.Measurement + A measurement combining a numeric value and a unit. + de.averbis.extraction.types.CoreAnnotation + + + unit + The unit of the measurement. + de.averbis.textanalysis.types.measurement.Unit + + + value + The numeric value of the measurement. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + normalizedUnit + Normalized string value of the unit. + uima.cas.String + + + normalizedAsciiUnit + Ascii normalized string value of the unit. + uima.cas.String + + + normalizedValue + The normalized value of the measurement. + This value is the result of the transformation of the numeric value according to the + transformation of the unit to its standard unit. + uima.cas.Double + + + normalized + The concatenation of the normalized numeric value and the ascii normalized unit. + uima.cas.String + + + parsedUnit + Optional parsable unit string which replaces the unit annotation. It is utilized + for normalization. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.MeasurementInterval + An interval defined by two measurements, a low and high limit. + de.averbis.extraction.types.CoreAnnotation + + + low + The lower bound of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + high + The upper bound of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + lowExcluded + Marker set to true if the lower bound itself is not part of the interval. + uima.cas.Boolean + + + highExcluded + Marker set to true if the upper bound itself is not part of the interval. + uima.cas.Boolean + + + + + de.averbis.textanalysis.types.measurement.NoUnit + A textual position that is not a unit. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.RelativeMeasurementInterval + A relative interval defined by two measurements, a base and deflection. + de.averbis.textanalysis.types.measurement.MeasurementInterval + + + base + The base of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + deflection + The deflection of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.measurement.SimpleMeasurementInterval + An interval extending MeasurementInterval with several primitive features + representing two measurements. + de.averbis.textanalysis.types.measurement.MeasurementInterval + + + lowNormalizedUnit + The normalized unit of the lower bound. + uima.cas.String + + + lowNormalizedValue + The normalized value of the lower bound. + uima.cas.Double + + + lowNormalized + The normalized value combined with the normalized unit of the lower bound. + uima.cas.String + + + lowParsedUnit + The parsed unit of the lower bound. + uima.cas.String + + + highNormalizedUnit + The normalized unit of the upper bound. + uima.cas.String + + + highNormalizedValue + The normalized value of the upper bound. + uima.cas.Double + + + highNormalized + The normalized value combined with the normalized unit of the upper bound. + uima.cas.String + + + highParsedUnit + The parsed unit of the upper bound. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.Unit + + de.averbis.extraction.types.CoreAnnotation + + + normalizedAscii + Ascii normalized string value of the unit. + uima.cas.String + + + parsed + String value of the parsed/identified unit. + uima.cas.String + + + normalized + Normalized string value of the unit. + uima.cas.String + + + dimension + The dimension of the unit in the form like '[L]^3' for volume + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.UnitParseAnchor + Helper type to use as anchor for unit parsing. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.numericvalue.ConjunctionFragment + A text span indicating a conjunction of numbers, which may also be located within + token like in 'fünfundzwanzig' + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.numericvalue.Fraction + A fraction of two NumericValue annotations. + de.averbis.extraction.types.CoreAnnotation + + + numerator + The numerator of the fraction. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + denominator + The denominator of the fraction. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.numericvalue.LanguageContainer + A container annotation specifying the language of the covered text. + de.averbis.extraction.types.CoreAnnotation + + + language + The language locale like 'de' or 'en'. + uima.cas.String + + + + + de.averbis.textanalysis.types.numericvalue.NumericValue + Represents a text span which can be interpreted as a numeric value which is stored + in a feature. + de.averbis.extraction.types.CoreAnnotation + + + value + The actual double value of the numeric value. + uima.cas.Double + + + + + de.averbis.textanalysis.types.numericvalue.RomanNumeral + Annotation for roman numerals. + de.averbis.extraction.types.CoreAnnotation + + + value + Integer value of the roman numeral. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.numericvalue.SimpleFraction + A fraction of two integer values. + de.averbis.extraction.types.CoreAnnotation + + + numerator + The numerator of the fraction. + uima.cas.Integer + + + denominator + The denominator of the fraction. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.temporal.Date + The expression describes a calendar time. + de.averbis.textanalysis.types.temporal.Timex3 + + + day + The day of the actual date. + uima.tcas.Annotation + + + month + The month of the actual date. + uima.tcas.Annotation + + + year + The year of the actual date. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.temporal.DateInterval + The expression describes an interval(or set) of dates defined + by the start and end date of an event. + de.averbis.textanalysis.types.temporal.TemporalSet + + + startDate + The start date of the temporal interval. + de.averbis.textanalysis.types.temporal.Date + + + endDate + The end date of the temporal interval. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.temporal.DayTime + Annotation indicating a time of day e.g., 'in the + morning'. + uima.tcas.Annotation + + + timeOfDay + Number specifying the time of the day. + uima.cas.String + + + + + de.averbis.textanalysis.types.temporal.DocumentDate + Annotation representing the date and time presenting the + document if available, e.g., + the creation time. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.Duration + The expression describes a duration. This value is + assigned to explicit durations. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.TemporalIntervalBeginIndicator + Indicator for a possible begin of a temporal interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.temporal.TemporalIntervalEndIndicator + Indicator for a possible end of a temporal interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.temporal.TemporalSet + The expression describes a set of times. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.Time + The expression refers to a time of the day, even if in a + very indefinite way. + de.averbis.textanalysis.types.temporal.Timex3 + + + hour + The hour of the actual time. + uima.tcas.Annotation + + + minute + The minute of the actual time. + uima.tcas.Annotation + + + second + The second of the actual time. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.temporal.Timex3 + Represents a text span which can be interpreted as a + numeric value which is stored in + a feature. + de.averbis.extraction.types.CoreAnnotation + + + tid + Non-optional attribute. Each TIMEX3 expression has to + be identified by a unique ID + number. This is automatically + assigned by the annotation tool. + uima.cas.String + + + kind + Non-optional attribute. Each TIMEX3 is assigned one of + the following types: DATE, + TIME, DURATION, or SET. The format of + the value attribute is determined by the type of TIMEX3. + For + instance, a DURATION must have a value that begins with the letter + ’P’ since durations + represent a period of time. This will be + elaborated on below in the value section. In addition, + some + optional attributes are used specifically with certain types of + temporal expressions. + uima.cas.String + + + value + The value attribute details which temporal information + is contained in the TIMEX3. + This value is given in an extended ISO + 8601 format. Examples: T24:00, 2001-01-12TEV, + 1984-01-03T12:00, + XXXX-12-02,1964-SU, P4M, PT20M + uima.cas.String + + + temporalFunction + Binary attribute which expresses that the value of the + temporal expression needs to + be determined via evaluation of a + temporal function. + uima.cas.Boolean + + + anchor + Optional attribute. It introduces the annotation of + the temporal expression to + which the TIMEX3 in question is + temporally anchored. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.temporal.UnambiguousTimex + Helper annotation type pointing to an most likely + unambiguous temporal expression. + The term '1992' could represent + a year, but also a measurement with that value. Other text spans like + '1.1.2015' are most likely + unambiguous dates, which can be represented + by this type. + de.averbis.extraction.types.CoreAnnotation + + + timex + The actual temporal expression. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.temporal.WeekDay + Annotation indicating a weekday e.g., 'Monday'. + uima.tcas.Annotation + + + dayOfWeek + Number of the day, e.g., 1 for Monday + uima.cas.Integer + + + + + de.averbis.textanalysis.types.text.ArrowCloseBracket + Annotation representing a arrow close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.ArrowOpenBracket + Annotation representing a arrow open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.Asterisk + Annotation representing an asterisk. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Backslash + Annotation representing a backslash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Bracket + Annotation representing a bracket. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Bullet + Annotation representing a bullet. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.CWord + Annotation representing a capitalized word including complex words composed of + multiple tokens. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Caret + Annotation representing a caret. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.CloseBracket + Annotation representing a close bracket. + de.averbis.textanalysis.types.text.Bracket + + + de.averbis.textanalysis.types.text.CurlyCloseBracket + Annotation representing a curly close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.CurlyOpenBracket + Annotation representing a curly open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.Dash + Annotation representing a dash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.DollarSign + Annotation representing a dollar sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.DoubleQuote + Annotation representing a double quote. + de.averbis.textanalysis.types.text.Quote + + + de.averbis.textanalysis.types.text.Equal + Annotation representing a equals sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.EuroSign + Annotation representing a euro sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.FirstInDocument + First token or fragment in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FirstInLine + First token or fragment in a line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FirstLine + First line in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FreeLine + First line of a paragraph that is preceded by an empty line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Hashtag + Annotation representing a hashtag. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.InBrackets + Annotation representing a text span in brackets (excluding arrow brackets). + de.averbis.textanalysis.types.text.TextSpan + + + de.averbis.textanalysis.types.text.InQuotes + Annotation representing a text span in quotes. + de.averbis.textanalysis.types.text.TextSpan + + + de.averbis.textanalysis.types.text.LastInDocument + Last token or fragment in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LastInLine + Last token or fragment in a line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LastLine + Last line in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LineFree + Last line of a paragraph that is followed by an empty line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Minus + Annotation representing a minus sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Num1 + Annotation representing a number with one digit. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num1_2 + Annotation representing a number with one or two digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num2 + Annotation representing a number with two digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num2_4 + Annotation representing a number with two to four digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num3 + Annotation representing a number with three digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num4 + Annotation representing a number with four digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num5 + Annotation representing a number with five digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.OpenBracket + Annotation representing a open bracket. + de.averbis.textanalysis.types.text.Bracket + + + de.averbis.textanalysis.types.text.Percent + Annotation representing a percent sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Plus + Annotation representing a plus sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Quote + Annotation representing a quote. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.RoundCloseBracket + Annotation representing a round close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.RoundOpenBracket + Annotation representing a round open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.SingleQuote + Annotation representing a single quote. + de.averbis.textanalysis.types.text.Quote + + + de.averbis.textanalysis.types.text.Slash + Annotation representing a slash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.SpecialChar + Annotation representing a special char. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.SquareCloseBracket + Annotation representing a square close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.SquareOpenBracket + Annotation representing a square open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.TextSpan + Annotation representing a text span. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Tilde + Annotation representing a tilde. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.TrimmedDocument + A trimmed version of the document annotation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Underscore + Annotation representing a underscore. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.VerticalBar + Annotation representing a vertical bar. + de.averbis.textanalysis.types.text.SpecialChar + + + org.apache.uima.ruta.type.ALL + + org.apache.uima.ruta.type.TokenSeed + + + org.apache.uima.ruta.type.AMP + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.ANY + + org.apache.uima.ruta.type.ALL + + + org.apache.uima.ruta.type.AnyLine + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.BREAK + + org.apache.uima.ruta.type.WS + + + org.apache.uima.ruta.type.CAP + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.COLON + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.COMMA + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.CW + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.DebugBlockApply + + org.apache.uima.ruta.type.DebugRuleApply + + + innerApply + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + + + + + org.apache.uima.ruta.type.DebugCreatedBy + + uima.cas.TOP + + + rule + + uima.cas.String + + + annotation + + uima.tcas.Annotation + + + script + + uima.cas.String + + + id + + uima.cas.Integer + + + + + org.apache.uima.ruta.type.DebugEvaluatedCondition + + uima.cas.TOP + + + element + + uima.cas.String + + + value + + uima.cas.Boolean + + + conditions + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + + + org.apache.uima.ruta.type.DebugFailedRuleMatch + + org.apache.uima.ruta.type.DebugRuleMatch + + + org.apache.uima.ruta.type.DebugInlinedBlock + + uima.cas.TOP + + + element + + uima.cas.String + + + asCondition + + uima.cas.Boolean + + + matched + + uima.cas.Boolean + + + inlinedRules + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + false + + + + + org.apache.uima.ruta.type.DebugMatchedRuleMatch + + org.apache.uima.ruta.type.DebugRuleMatch + + + org.apache.uima.ruta.type.DebugRuleApply + + org.apache.uima.ruta.type.DebugScriptApply + + + applied + + uima.cas.Integer + + + tried + + uima.cas.Integer + + + rules + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleMatch + + + id + + uima.cas.Integer + + + script + + uima.cas.String + + + + + org.apache.uima.ruta.type.DebugRuleElementMatch + + org.apache.uima.ruta.type.ProfiledAnnotation + + + baseCondition + + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + conditions + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + elements + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatches + false + + + inlinedConditionBlocks + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugInlinedBlock + false + + + + + org.apache.uima.ruta.type.DebugRuleElementMatches + + uima.cas.TOP + + + matches + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatch + + + element + + uima.cas.String + + + ruleAnchor + + uima.cas.Boolean + + + inlinedActionBlocks + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugInlinedBlock + false + + + + + org.apache.uima.ruta.type.DebugRuleMatch + + org.apache.uima.ruta.type.ProfiledAnnotation + + + elements + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatches + + + matched + + uima.cas.Boolean + + + delegates + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + + + + + org.apache.uima.ruta.type.DebugScriptApply + + org.apache.uima.ruta.type.ProfiledAnnotation + + + element + + uima.cas.String + + + timestamp + + uima.cas.Long + + + + + org.apache.uima.ruta.type.EXCLAMATION + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.EmptyLine + + org.apache.uima.ruta.type.AnyLine + + + org.apache.uima.ruta.type.EvalAnnotation + + uima.tcas.Annotation + + + original + The annotation that caused this outcome. + uima.tcas.Annotation + + + group + Identifier for the group of annotations and types in the evaluation. + uima.cas.String + + + + + org.apache.uima.ruta.type.FalseNegative + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.FalsePositive + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.Line + + org.apache.uima.ruta.type.AnyLine + + + org.apache.uima.ruta.type.MARKUP + + org.apache.uima.ruta.type.ALL + + + org.apache.uima.ruta.type.NBSP + + org.apache.uima.ruta.type.SPACE + + + org.apache.uima.ruta.type.NUM + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.PERIOD + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.PM + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.Paragraph + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.ProfiledAnnotation + + uima.tcas.Annotation + + + time + + uima.cas.Long + + + + + org.apache.uima.ruta.type.QUESTION + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.RutaAnnotation + + uima.tcas.Annotation + + + score + + uima.cas.Double + + + annotation + + uima.tcas.Annotation + + + + + org.apache.uima.ruta.type.RutaBasic + + uima.tcas.Annotation + + + replacement + + uima.cas.String + + + + + org.apache.uima.ruta.type.RutaColoring + + uima.tcas.Annotation + + + bgColor + + uima.cas.String + + + targetType + + uima.cas.String + + + fgColor + + uima.cas.String + + + selected + + uima.cas.Boolean + + + + + org.apache.uima.ruta.type.RutaFrame + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.RutaOptional + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.SEMICOLON + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.SENTENCEEND + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.SPACE + + org.apache.uima.ruta.type.WS + + + org.apache.uima.ruta.type.SPECIAL + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.SW + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.Statistics + + uima.cas.TOP + + + name + + uima.cas.StringArray + + + total + + uima.cas.DoubleArray + + + amount + + uima.cas.IntegerArray + + + part + + uima.cas.DoubleArray + + + + + org.apache.uima.ruta.type.TokenSeed + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.TruePositive + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.W + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.WS + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.WSLine + + org.apache.uima.ruta.type.EmptyLine + + + org.apache.uima.ruta.type.html.A + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.B + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BIG + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BODY + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BR + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.COMMENT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.DIV + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.EM + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.FONT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.FORM + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H1 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H2 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H3 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H4 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H5 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H6 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.HEAD + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.HTML + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.I + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.IMG + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.INPUT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.LI + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.LINK + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.META + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.OL + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.P + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.REMARK + + org.apache.uima.ruta.type.html.TAG + + + comment + + uima.cas.String + + + + + org.apache.uima.ruta.type.html.SCRIPT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.SMALL + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.SPAN + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.STYLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TABLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TAG + + uima.tcas.Annotation + + + name + + uima.cas.String + + + expandedOffsets + + uima.cas.Boolean + + + attributeName + + uima.cas.StringArray + false + + + attributeValue + + uima.cas.StringArray + false + + + + + org.apache.uima.ruta.type.html.TBODY + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TD + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TH + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TITLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TR + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.U + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.UL + + org.apache.uima.ruta.type.html.TAG + + + + + + org.apache.uima.ruta.type.RutaFrame + uima.tcas.Annotation + org.apache.uima.ruta.type.RutaBasic + + + + + + true + true + false + + + diff --git a/src/test/resources/projects/it1/reference/pom.xml b/src/test/resources/projects/it1/reference/pom.xml index 5522d35..eca5ec0 100644 --- a/src/test/resources/projects/it1/reference/pom.xml +++ b/src/test/resources/projects/it1/reference/pom.xml @@ -71,6 +71,27 @@ numeric-value-typesystem ${core-typesystems-version} + + de.averbis.textanalysis + named-entity-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + text-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + neural-typesystem + ${core-typesystems-version} + + + de.averbis.textanalysis + evaluation-typesystem + ${core-typesystems-version} + + de.averbis.textanalysis @@ -190,27 +211,6 @@ - - org.codehaus.mojo - exec-maven-plugin - 1.6.0 - - - generate-ruta-template - process-classes - - java - - - com.example.nlp.GenerateConfiguredDescriptorTemplate - test - - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml - - - - - org.apache.uima ruta-maven-plugin @@ -218,7 +218,7 @@ descriptors - process-classes + generate-sources generate @@ -229,7 +229,7 @@ **/*.ruta - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml + ${basedir}/src/main/resources/descriptor/GeneratedBasicEngine.xml ${project.build.directory}/generated-sources/ruta/descriptor ${project.build.directory}/generated-sources/ruta/descriptor RutaAnnotator @@ -248,6 +248,31 @@ + + + org.apache.uima + jcasgen-maven-plugin + ${uima-version} + + + generate-jcas-classes + generate-sources + + generate + + + + target/generated-sources/ruta/descriptor/com/example/nlp/ContractRutaTypeSystem.xml + + + /**/BasicTypeSystem.xml + /**/InternalTypeSystem.xml + + true + + + + org.apache.maven.plugins maven-resources-plugin @@ -295,6 +320,7 @@ + org.apache.maven.plugins maven-dependency-plugin @@ -313,13 +339,13 @@ + org.apache.uima PearPackagingMavenPlugin ${uima-version} true - package @@ -334,35 +360,6 @@ - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.codehaus.mojo - exec-maven-plugin - [1.6.0,) - - java - - - - - - - - - - - - diff --git a/src/test/resources/projects/it1/reference/src/main/java/com/example/nlp/GenerateConfiguredDescriptorTemplate.java b/src/test/resources/projects/it1/reference/src/main/java/com/example/nlp/GenerateConfiguredDescriptorTemplate.java index b7f6113..e70ca10 100644 --- a/src/test/resources/projects/it1/reference/src/main/java/com/example/nlp/GenerateConfiguredDescriptorTemplate.java +++ b/src/test/resources/projects/it1/reference/src/main/java/com/example/nlp/GenerateConfiguredDescriptorTemplate.java @@ -31,12 +31,17 @@ import org.apache.uima.ruta.engine.RutaEngine; import org.xml.sax.SAXException; +/** + * Helper class for manually generating a preconfigured descriptor template for the generated Ruta + * analysis engine descriptors + * + */ public class GenerateConfiguredDescriptorTemplate { public static void main(String[] args) throws ResourceInitializationException, FileNotFoundException, SAXException, IOException { - File outputFile = new File(args[0]); + File outputFile = new File("src/main/resources/descriptor/GeneratedBasicEngine.xml"); outputFile.getParentFile().mkdirs(); AnalysisEngineDescription description = AnalysisEngineFactory diff --git a/src/test/resources/projects/it1/reference/src/main/resources/descriptor/GeneratedBasicEngine.xml b/src/test/resources/projects/it1/reference/src/main/resources/descriptor/GeneratedBasicEngine.xml new file mode 100644 index 0000000..d5716b2 --- /dev/null +++ b/src/test/resources/projects/it1/reference/src/main/resources/descriptor/GeneratedBasicEngine.xml @@ -0,0 +1,6098 @@ + + + org.apache.uima.java + true + org.apache.uima.ruta.engine.RutaEngine + + org.apache.uima.ruta.engine.RutaEngine + Descriptor automatically generated by uimaFIT + unknown + org.apache.uima.ruta.engine + + + rules + + String + false + false + + + rulesScriptName + + String + false + true + + + mainScript + + String + false + false + + + scriptEncoding + + String + false + false + + + scriptPaths + + String + true + false + + + descriptorPaths + + String + true + false + + + resourcePaths + + String + true + false + + + additionalScripts + + String + true + false + + + additionalEngines + + String + true + false + + + additionalUimafitEngines + + String + true + false + + + additionalExtensions + + String + true + false + + + reloadScript + + Boolean + false + false + + + seeders + + String + true + false + + + defaultFilteredTypes + + String + true + false + + + removeBasics + + Boolean + false + false + + + dynamicAnchoring + + Boolean + false + false + + + lowMemoryProfile + + Boolean + false + false + + + simpleGreedyForComposed + + Boolean + false + false + + + greedyRuleElement + + Boolean + false + false + + + greedyRule + + Boolean + false + false + + + debug + + Boolean + false + false + + + debugWithMatches + + Boolean + false + false + + + debugAddToIndexes + + Boolean + false + false + + + debugOnlyFor + + String + true + false + + + profile + + Boolean + false + false + + + statistics + + Boolean + false + false + + + createdBy + + Boolean + false + false + + + strictImports + + Boolean + false + false + + + typeIgnorePattern + + String + false + false + + + dictRemoveWS + + Boolean + false + false + + + csvSeparator + + String + false + false + + + varNames + + String + true + false + + + varValues + + String + true + false + + + indexOnly + + String + true + false + + + reindexOnly + + String + true + false + + + indexOnlyMentionedTypes + + Boolean + false + true + + + reindexOnlyMentionedTypes + + Boolean + false + true + + + indexSkipTypes + + String + true + true + + + reindexSkipTypes + + String + true + true + + + indexAdditionally + + String + true + false + + + reindexAdditionally + + String + true + false + + + reindexUpdateMode + + String + false + true + + + validateInternalIndexing + + Boolean + false + true + + + emptyIsInvisible + + Boolean + false + false + + + modifyDataPath + + Boolean + false + false + + + inferenceVisitors + + String + true + false + + + maxRuleMatches + + Integer + false + false + + + maxRuleElementMatches + + Integer + false + false + + + + + rulesScriptName + + Anonymous + + + + scriptEncoding + + UTF-8 + + + + descriptorPaths + + + + + + resourcePaths + + + + + + additionalScripts + + + + + + additionalEngines + + + + + + additionalUimafitEngines + + + + + + additionalExtensions + + + + + + reloadScript + + false + + + + seeders + + + org.apache.uima.ruta.seed.TextSeeder + + + + + defaultFilteredTypes + + + org.apache.uima.ruta.type.SPACE + org.apache.uima.ruta.type.BREAK + org.apache.uima.ruta.type.MARKUP + + + + + removeBasics + + false + + + + dynamicAnchoring + + false + + + + lowMemoryProfile + + false + + + + simpleGreedyForComposed + + false + + + + greedyRuleElement + + false + + + + greedyRule + + false + + + + debug + + false + + + + debugWithMatches + + false + + + + debugAddToIndexes + + false + + + + debugOnlyFor + + + + + + profile + + false + + + + statistics + + false + + + + createdBy + + false + + + + strictImports + + false + + + + dictRemoveWS + + true + + + + csvSeparator + + ; + + + + varNames + + + + + + varValues + + + + + + indexOnly + + + uima.tcas.Annotation + + + + + reindexOnly + + + uima.tcas.Annotation + + + + + indexOnlyMentionedTypes + + false + + + + reindexOnlyMentionedTypes + + false + + + + indexSkipTypes + + + + + + reindexSkipTypes + + + + + + indexAdditionally + + + + + + reindexAdditionally + + + + + + reindexUpdateMode + + COMPLETE + + + + validateInternalIndexing + + false + + + + emptyIsInvisible + + true + + + + modifyDataPath + + false + + + + inferenceVisitors + + + + + + maxRuleMatches + + 2147483647 + + + + maxRuleElementMatches + + 2147483647 + + + + + + + de.averbis.extraction.types.Abbreviation + An abbreviation is a letter or group of letters, taken from a word or words. For + example, the word "abbreviation" can be abbreviated as "abbr." or "abbrev." + de.averbis.extraction.types.CoreAnnotation + + + fullForm + The full form of an abbreviation. The full form, for example for HLA could be + human leukocyte antigen. + uima.cas.String + + + textReference + Reference to the text span that contains the full form of the + abbreviation/acronym. + de.averbis.extraction.types.CoreAnnotation + + + definedHere + This feature is true if the abbreviation/acronym is defined for the first time in + the text, e.g. in "interleukin 2 (Il-2) receptor", it can be true only for locally introduced + abbreviations/acronyms. + uima.cas.Boolean + + + stems + Stems of the full form. + uima.cas.StringArray + true + + + segments + Segments of the full form. + uima.cas.StringArray + true + + + tokens + Token strings of the full form. + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Abstract + Semantic abstract section found in the text. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Category + Category meta information on the document or a region of this document (use the + context feature to identify which section this category refers to). E.g. language information of + the document text or language information of specific sections. + de.averbis.extraction.types.CoreAnnotation + + + group + The category group (e.g. HSG, language) to which from which the label belongs. + For language categorization the group might be "lang" and then the labels could be "en", "de", + "fr" etc. + uima.cas.String + + + label + The label of the category annotation. E.g. in the case that we identified + languages (de, en, fr, ...). + uima.cas.String + + + context + The text context which belongs to the given category annotation, e.g. Document, + Section, Sentence. + de.averbis.extraction.types.CoreAnnotation + + + rank + The rank of the current category with respect to the context. + uima.cas.Integer + + + + + de.averbis.extraction.types.Chunk + A general type for chunks (NPs, VPs, PPs etc.). + Note: there are 3 specific subtypes for common chunks: ChunkNP, ChunkVP, ChunkPP. + For all other chunk types (e.g., SBAR; ADJP etc.) use this general type! + de.averbis.extraction.types.CoreAnnotation + + + enclosedTokens + The Token annotations enclosed by this chunk. + uima.cas.Integer + + + head + The head entity on which this chunk grammatically depends. Example: in "Der Vater + des Kindes" is "der Vater" the head of "des Kindes". + de.averbis.extraction.types.CoreAnnotation + + + dependents + The entities which grammatically depend on this chunk. Example: in "Der Vater des + Kindes" is "des Kindes" the dependent of "Der Vater". + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + value + The specific chunk tag as returned by the chunker (e.g., "NP", "SBAR", "S" etc.). + uima.cas.String + + + + + de.averbis.extraction.types.ChunkNP + A noun phrase (e.g. "the strange bird"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.ChunkPP + A prepositional phrase (e.g. "in between"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.ChunkVP + A verb phrase (e.g. "has been thinking"). + de.averbis.extraction.types.Chunk + + + de.averbis.extraction.types.Concept + A concept is a reference to an entry in a database, terminology, taxonomy, ontology + etc. + de.averbis.extraction.types.CoreAnnotation + + + dictCanon + Canonical form (preferred term). + uima.cas.String + + + enclosingSpan + The span that this concept is contained within (i.e. its sentence). + de.averbis.extraction.types.CoreAnnotation + + + negatedBy + Indicates which annotation negates the concept. + de.averbis.extraction.types.CoreAnnotation + + + partialMatch + Specifies if the annotation matches the complete context. + E.g. if coveredText is "Lungenabschnitte" and the generated Concept annotation is "Lunge", then + this value is set to true. + uima.cas.Boolean + + + matchedText + The text in document which matched the synonym (in the respective mapping mode + form, i.e., segment/stem/original etc.). + uima.cas.String + + + matchedTerm + The synonym of the concept which caused the match (in the + ConceptAnnotator-dictionary this is <term label=xxx>). + uima.cas.String + + + matchedVariant + The variant of the synonym of the concept which caused the match (in the + ConceptAnnotator-dictionary this is <variant label=xxx>). + Note that one synonym (matchedTerm) can have several variants (i.e. spelling forms or mapping + forms). + uima.cas.String + + + matchedTokens + The Token annotations on which the concept was found. + Note that there is also matchedAnnotations which list the actual annotations involved in the + matching process (i.e., token, stem, segment, etc.). + uima.cas.FSArray + de.averbis.extraction.types.Token + true + + + matchedAnnotations + List of the actual annotations involved in the matching process (i.e., original, + stem, segment, etc.). + Note that there is also matchedTokens, which lists only matching Token annotations. + uima.cas.FSArray + true + + + mappingMode + The mode used for mapping (e.g., original, stem, segment...). + uima.cas.String + + + mappingFuzzynessScore + The score for the fuzzyness of the mapping (higher scores mean higher fuzzyness, + i.e., less exact mappings). + uima.cas.Float + + + uniqueID + The unique concept id, including terminology name and concept ID + should look like this: <terminologyName>:<conceptID>. + uima.cas.String + + + conceptID + The concept id. For a unique id refer to uniqueID. + uima.cas.String + + + source + The name of the terminology source. + uima.cas.String + + + + + de.averbis.extraction.types.CoreAnnotation + The base type for all annotation types providing a componentId and confidence. + uima.tcas.Annotation + + + componentId + The id/name of the component that created this annotation. + uima.cas.String + + + confidence + Confidence value of the current annotation. E.g. in the case the annotation has + been created by a statistical analysis engine. + uima.cas.Double + + + confidenceKind + Additional information about the specific kind of confidence. This provides an + option to indicate if the confidence feature is set at all. + uima.cas.String + + + + + de.averbis.extraction.types.Descriptor + An index term from an ontology; its type (or reference) is written in the feature + annotation. + de.averbis.extraction.types.IndexTerm + + + uid + The unique identifier of the descriptor, e.g., a combination of terminology and + concept id. + uima.cas.String + + + + + de.averbis.extraction.types.Entity + A named entity; not to be confused with a Concept. A (named) entity is a string + representation in text referring to a class of entities. Thus, the entity mention does not have + an identifier but a specific type (the category) assigned to it. + de.averbis.extraction.types.CoreAnnotation + + + value + This feature provides the text of the annotated mention. Important for easily + representing discontinuous mentions such as 'T cell' in the expression 'T and B cell'. + uima.cas.String + + + label + The type of the entity; e.g., PERSON, LOCATION etc. + Feature name is label due to the fact that "type" is a reserved word. + uima.cas.String + + + parsedElements + Reference to all recognized entities inside this Entity such as Size, Time, Area, + Date, Volume, .... + uima.cas.FSArray + de.averbis.extraction.types.Entity + true + + + + + de.averbis.extraction.types.Enumeration + A specific group representing an enumeration like "red, blue and green". + de.averbis.extraction.types.Group + + + de.averbis.extraction.types.GenericMetadata + Type holding generic metadata information of a document. Multiple annotations should + be used to add additional metadata to the CAS. + de.averbis.extraction.types.CoreAnnotation + + + metadataFieldname + To reduce the potential metadata field names, the predefined field names should be + used where possible (add new field names if necessary). + Predefined metadata field names are: title, summary, filesize, annotatorName. + uima.cas.String + + + value + Value of the metadata field, e.g. + metadataFieldname = title, + value = "Brave new world". + uima.cas.String + + + + + de.averbis.extraction.types.Group + Groups together a set of annotations that belong together, e.g., enumerations. One + of them can be set to the "leading" concept. + E.g. "the liver metastasis is hypodense and has a size of 3cm*2cm". + lead: metastasis, other concepts: liver, hypodense, 3cm*2cm + de.averbis.extraction.types.CoreAnnotation + + + leadingAnnotation + Optional annotation indicating the leading head of hte group. + de.averbis.extraction.types.CoreAnnotation + + + members + Annotations contained in the group. + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + label + Textual label describing the group elements. + uima.cas.String + + + + + de.averbis.extraction.types.Header + The header annotation of a document + de.averbis.extraction.types.CoreAnnotation + + + docID + The ID of the document. + uima.cas.String + + + source + The source of the document. + uima.cas.String + + + path + The path of the document. + uima.cas.String + + + fileName + The name of the source file (often used by cas consumers which produce an output + file for each CAS; this name is used as base). + uima.cas.String + + + fileEncoding + The encoding of the file. + uima.cas.String + + + documentIndex + The current number of the documents, i.e. a document is number 5 in a complete + sequence. + uima.cas.Integer + + + lastFile + Indicates if this is the last file. + uima.cas.Boolean + + + sourceLanguage + The document language of the source. + uima.cas.String + + + offsetInSource + Byte offset of the start of document content within original source file or other + input source. Only used if the CAS document was retrieved from an source where one physical + source file contained several conceptual documents. Zero otherwise. + uima.cas.Integer + + + documentSize + Size of original document in bytes before processing by CAS Initializer. Either + absolute file size of size within file or other source. + uima.cas.Integer + + + sequenceNumber + Sequence number to test the right order while merging CASes. + uima.cas.Integer + + + lastSegment + For a CAS that represents a segment of a larger source document, this flag + indicates whether this CAS is the final segment of the source document. This is useful for + downstream components that want to take some action after having seen all of the segments of a + particular source document. + uima.cas.Boolean + + + + + de.averbis.extraction.types.IndexTerm + A term to be used for indexing a document. + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the index term. Example: the normalized and stemmed + string which represents a keyword in the free keywording scenario or for controlled keywording + (=descriptor extraction) the dictCanon might be written here. + uima.cas.String + + + baseAnnotation + The annotation to be assigned as index term. This can i.e. be a Concept or a Noun + Phrase annotation from which the index term was derived. + de.averbis.extraction.types.CoreAnnotation + + + + + de.averbis.extraction.types.InputParam + InputParam is used to pass parameters to an analysis engine via a JCas object. This + may be used to pass parameters + in the process() method of an analysis engine rather than during initialization of the AEs. It is + e.g. necessary + for the ConceptAnnotator at which you want to pass restrictions (such as "language" or + "terminology") for each single + text/jcas while only having one ConceptAnnotator instance. + de.averbis.extraction.types.CoreAnnotation + + + key + The key of the input parameter. + uima.cas.String + + + values + The values of the input parameter. + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Keyword + A keyword that is assigned freely (i.e., not taken from an ontology) to a document. + Its type is written in the feature annotation + de.averbis.extraction.types.IndexTerm + + + de.averbis.extraction.types.Lemma + Lemma is the canonical form of a lexeme. Lemmata can be retrieved from lexicon or be + produced by lemmatizer. + de.averbis.extraction.types.CoreAnnotation + + + value + The value of the lemma. + uima.cas.String + + + case + Case such as Nom (Nominative) or Gen (Genitive) etc. + uima.cas.String + + + number + Singular or plural. + uima.cas.String + + + gender + fem or masc or neutr. + uima.cas.String + + + + + de.averbis.extraction.types.Listing + A specific group representing a listing like "1. red 2. blue 3. green". + de.averbis.extraction.types.Group + + + de.averbis.extraction.types.Member + Utility annotation for indicating a member of a group. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.extraction.types.POSTag + Parent type for all specific part-of-speech types. + de.averbis.extraction.types.CoreAnnotation + + + tagsetId + The name of the tag set the pos tag belongs to; e.g. the "Penn Treebank II Tags" + (see http://bulba.sdsu.edu/jeanette/thesis/PennTags.html) + uima.cas.String + + + value + The specific part-of-speech tag, as returned by the POS-Tagger (e.g., "NN" or + "ADJ" etc) + uima.cas.String + + + + + de.averbis.extraction.types.POSTagAdj + The type for all POS-Tags of the type "Adjective". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagAdp + The type for all POS-Tags of the type "Preposition/Postposition". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagAdv + The type for all POS-Tags of the type "Adverb". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagConj + The type for all POS-Tags of the type "Conjunction". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagDet + The type for all POS-Tags of the type "Determiner". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagNoun + The type for all POS-Tags of the type "Noun". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagNum + The type for all POS-Tags of the type "Numeral". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPart + The type for all POS-Tags of the type "Particle". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPron + The type for all POS-Tags of the type "Pronoun". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagPunct + The type for all POS-Tags of the type "Punctuation". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.POSTagVerb + The type for all POS-Tags of the type "Verb". + de.averbis.extraction.types.POSTag + + + de.averbis.extraction.types.Paragraph + Different paragraphs found in the document. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Relation + Describes a binary relation between two annotations. + The relation is defined according to the SPO (subject, predicate, object) annotation. + de.averbis.extraction.types.CoreAnnotation + + + subject + An annotation representing the subject of the relation ("agens"). + de.averbis.extraction.types.CoreAnnotation + + + predicate + The annotation representing the predicate of the relation + e.g. + BASF has integrated BAYER + --> 'has integrated' is the predicate that is marked as ChunkVP + --> use the feature 'value' to define the type of the relation + --> value: acquisition + de.averbis.extraction.types.CoreAnnotation + + + object + The object of the relation. + de.averbis.extraction.types.CoreAnnotation + + + value + Type of the relation. + uima.cas.String + + + + + de.averbis.extraction.types.ResolvedEntity + A special entity with an additional specific resolved form. + de.averbis.extraction.types.Entity + + + resolvedType + The type of the resolved form. + uima.cas.String + + + resolvedForm + A string representing the resolved form of the entity. + uima.cas.String + + + + + de.averbis.extraction.types.Section + Text sections of a certain type. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Segment + The segmentation of a text part; a segment is usually a subword (i.e., part of a + token). + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the segment. + uima.cas.String + + + isValidSegmentation + Indicates if the segmentation is valid (viz. could be completely matched against + the dictionary). + uima.cas.Boolean + + + midStrings + The MID value, multiple for ambiguous MIDs (for MID see Morphosaurus Paper). + uima.cas.StringArray + true + + + + + de.averbis.extraction.types.Sentence + Annotation representing a sentence including the ending punctuation mark. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.extraction.types.Stem + The type for stem annotations. + de.averbis.extraction.types.CoreAnnotation + + + value + The string representation of the stem. + uima.cas.String + + + + + de.averbis.extraction.types.SummarySentence + Annotation indicating a sentence that makes up a summary of the document. + de.averbis.extraction.types.CoreAnnotation + + + sentence + The sentence annotation that contains the content of this summary sentence. + de.averbis.extraction.types.Sentence + + + descriptors + The descriptors extracted by the algorithm accounting to the selection of the + sentence. + uima.cas.FSArray + de.averbis.extraction.types.Descriptor + true + + + + + de.averbis.extraction.types.Title + Marks a title in the document. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Token + Annotation for basic textual units including word, numbers and punctuation marks. + de.averbis.extraction.types.CoreAnnotation + + + posTag + The part of speech of this token (i.a. used for concept annotator to be restricted + to certain pos types). + de.averbis.extraction.types.POSTag + + + segments + Segments of this token (i.a. used for respective mode in concept annotator). + uima.cas.FSArray + de.averbis.extraction.types.Segment + true + + + stem + The stem of the token (i.a. used for respective mode in concept annotator). + de.averbis.extraction.types.Stem + + + isAbbreviation + Marker whether the token is (part of) an abbreviation. + uima.cas.Boolean + + + abbreviations + The abbreviations for the token; this may be used as replacement in concept + annotator. Note, that this goes in combination with "isAbbreviation" marking whether the token + is an abbreviation. + Multiple entries mean that there is ambiguity which full form is correct. There will be components to + resolve this ambiguity which then remove wrong forms. + Components which cannot do this ambiguity resolution must rely that the first (and hopefully only) entry + is correct! + uima.cas.FSArray + de.averbis.extraction.types.Abbreviation + true + + + ignoreByConceptMapper + If this feature is true then the ConceptAnnotator + ignores the token. Use this is a pre-processing + component has already identified the semantic of + the token. E.g. dates, times, measurement values. + Default value: false + uima.cas.Boolean + + + normalized + Normalized version of this token (usually lower-case, without special characters + and number). + uima.cas.String + + + diacriticsFreeVersions + In the case that the normalized version contains diacritics, multiple versions + without diacritics are stored in this array. + uima.cas.StringArray + true + + + isStopword + Indicates if the token is a stopword. + uima.cas.Boolean + + + lemma + The Lemma of the token. + de.averbis.extraction.types.Lemma + + + isInvariant + Defines whether a token is an invariant. Such a token should not undergo some + morphologic analysis steps, such as stemming and/or decompounding. + However, lemmatization might still be allowed. + Typical invariants: IL-2 (gene name) or also product names or numbers (SR-2715) but also too short + words (au). + uima.cas.Boolean + + + tokenClass + The optional string representing the class of the token concerning its surface + form. + uima.cas.String + + + + + de.averbis.extraction.types.ValidTextSegment + Zone to mark valid text in contrast to invalid text which e.g. may be OCR (Optical + Character Recognition) artefacts, number blocks, tables etc. + de.averbis.extraction.types.Zone + + + de.averbis.extraction.types.Zone + An annotation concerning the document structure, e.g. header, title, abstract, etc. + de.averbis.extraction.types.CoreAnnotation + + + label + Allows to annotated the Zone with a semantic label. + E.g. in the case of a section the value might be + Introduction, Appendix,... + uima.cas.String + + + weight + The relevance or weight for a zone; used e.g. to weight information contained in + the respective zone. + uima.cas.Float + + + + + de.averbis.textanalysis.types.AbstractName + The name of a person. + de.averbis.extraction.types.Entity + + + reference + Textual reference of the name. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.AnnotationClassification + General classification result on annotation level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.AnnotationScope + Scope of a cue annotation. + de.averbis.extraction.types.CoreAnnotation + + + label + Optional label indicating the kind of scope. + uima.cas.String + + + cue + The cue indicating the scope. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.ConceptEmbedding + Represents a concept embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.DocumentClassification + General classification result on document level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.DocumentEmbedding + Represents a document embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.Embedding + Represents an embedding for a given target annotation. + de.averbis.extraction.types.CoreAnnotation + + + vector + The actual dense embedding vector. + uima.cas.DoubleArray + true + + + dimension + The dimension of the embedding. + uima.cas.Integer + + + kind + The kind of the embedding. + uima.cas.String + + + id + Identifier representing the embedding model. + uima.cas.String + + + reference + The original annotation represented by the embedding. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.FirstName + The first name. + de.averbis.textanalysis.types.AbstractName + + + de.averbis.textanalysis.types.GenericClassification + A classification result. + de.averbis.extraction.types.CoreAnnotation + + + group + Group indicating the classification context. + uima.cas.String + + + label + Label indicating the classification result. + uima.cas.String + + + annotation + Optional reference to the classified annotation or category. + uima.tcas.Annotation + + + featureImpacts + Optional information concerning the weight/importance/impact of specific features. + uima.cas.StringArray + true + + + relevantSpans + Optional information concerning the position of relevant spans. + uima.cas.FSArray + de.averbis.textanalysis.types.PredictionRelevantSpan + true + + + + + de.averbis.textanalysis.types.GenericCue + A generic cue. + de.averbis.extraction.types.CoreAnnotation + + + label + Optional label indicating the kind of cue. + uima.cas.String + + + + + de.averbis.textanalysis.types.LastName + The last name. + de.averbis.textanalysis.types.AbstractName + + + de.averbis.textanalysis.types.ParagraphEmbedding + Represents a paragraph embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.PersonName + The name of a person. + de.averbis.textanalysis.types.AbstractName + + + firstName + Person's first name. + de.averbis.textanalysis.types.FirstName + + + lastName + Person's last name. + de.averbis.textanalysis.types.LastName + + + + + de.averbis.textanalysis.types.PredictionRelevantSpan + A span pointing to relevant annotations for a specific classification. + de.averbis.extraction.types.CoreAnnotation + + + relatedAnnotations + Relevant source annotations. + uima.cas.FSArray + uima.tcas.Annotation + true + + + featureImpacts + Relevant features for identifying this span. + uima.cas.StringArray + true + + + + + de.averbis.textanalysis.types.RelationClassification + General classification result on annotation relation level. + de.averbis.textanalysis.types.GenericClassification + + + de.averbis.textanalysis.types.SentenceEmbedding + Represents a sentence embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.WordEmbedding + Represents a word embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + de.averbis.textanalysis.types.Wordpiece + A tokenized part of a word. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized (and lowercased) version of the wordpiece without accents. + uima.cas.String + + + embedding + Optional embedding of this wordpiece. + de.averbis.textanalysis.types.WordpieceEmbedding + + + tokenStart + Flag indicating that the word piece is located at the beginning of a token. + uima.cas.Boolean + + + tokenStartWordpiece + Optional reference to additional wordpiece representing the start of a token. + de.averbis.textanalysis.types.Wordpiece + + + vocabularyIndex + Index of wordpiece in the vocabulary. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.WordpieceEmbedding + Represents a wordpiece embedding for a given target annotation. + de.averbis.textanalysis.types.Embedding + + + tokenStartEmbedding + Optional embedding of an additional token start wordpiece. + de.averbis.textanalysis.types.WordpieceEmbedding + + + + + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + Parent type for all evaluation types which is able to store a reference annotation. + de.averbis.extraction.types.CoreAnnotation + + + annotation + The corresponding annotation. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.evaluation.FalseNegative + An annotation was not found but should have been found. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.FalsePositive + An annotation was found but should not have been found. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.PartialPositive + A partially correct annotation. + de.averbis.textanalysis.types.evaluation.TruePositive + + + de.averbis.textanalysis.types.evaluation.SimilarityMatching + Various information of candidate matches for debugging purposes. + de.averbis.extraction.types.CoreAnnotation + + + candidate + The corresponding annotation. + uima.tcas.Annotation + + + predicted + All predicted labels for candidate. + uima.cas.StringArray + true + + + + + de.averbis.textanalysis.types.evaluation.TrueNegative + A correctly missing annotation. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.evaluation.TruePositive + A correct annotation. + de.averbis.textanalysis.types.evaluation.EvaluationAnnotation + + + de.averbis.textanalysis.types.health.Abnormal + Abnormal observation. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + de.averbis.textanalysis.types.health.AbstractDrug + Supertype of the drugs. + de.averbis.extraction.types.CoreAnnotation + + + brandName + The brand name of the drug. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.AbstractInterpretation + Abstract supertype for interpretations. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AbstractObservation + Abstract type for observations, like laboratory values, vital signs, etc. + de.averbis.extraction.types.CoreAnnotation + + + parameter + The actual parameter of the observation. + de.averbis.extraction.types.Concept + + + date + The date of the observation. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + Abstract type for lymph node mentions. + de.averbis.textanalysis.types.health.TNMBasic + + + attacked + Number of attacked lymph nodes. + uima.cas.Integer + + + tested + Number of tested lymph nodes. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.AdditionalDoseAmount + Textspan specifying additional information of the dose amount. + de.averbis.extraction.types.CoreAnnotation + + + value + The numeric value describing the additional amount. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.AdditionalDoseAmountIndicator + Indicator for following additional dose amount. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Administration + Textspan specifying a route of administration. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AdmissionDateInd + Indicator for a following admission date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.AdmissionDiagnosisSection + Section containing information about diagnosis on admission. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AdmissionMedicationSection + Admission can refer to hospital admission, long-term care admission, or home health admission. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.AdmissionReasonSection + This section records the patient's reason for their visit (the provider's description of the reason + for visit). Local policy determines whether the information is divided into two sections or recorded + in one section serving both purposes. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AdverseEventSection + Contains a list and description of any allergies or adverse reactions pertinent to current or past + medical history. At a minimum this section should contain currently active and any relevant historical + allergies and adverse reactions. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.AnamnesisSection + History general describes all aspects of medical history of the patient even if not pertinent to the + current procedure, and may include chief complaint, past medical history, social history, family + history, surgical or procedure history, medication history, and other history information. + The history may be limited to information pertinent to the current procedure or may be more + comprehensive. It may also be reported as a collection of random clinical statements or it may be + reported categorically. Categorical report formats may be divided into multiple subsections, including + Past Medical History and Social History. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.AngiogramSection + Section containing information about angiogram. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.AnteriorEyeSegmentSection + Section containing information about the anterior eye segment. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.BiologicalProductConcept + Concept type for the material of a biologically derived product. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.BiologicallyDerivedProduct + A material substance originating from a biological entity intended + to be transplanted or infused into another (possibly the same) biological entity. + Example: hematopoietic stem cells. + de.averbis.extraction.types.CoreAnnotation + + + product + The material concept of the product. + de.averbis.extraction.types.Concept + + + quantity + The quantity of the biologically derived product. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + time + Date or time of the transplantation. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.health.BiopsyIndicator + Indicators that document contains biopsy report. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BirthDateIndicator + Indicator for a following birth date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BloodPressure + Annotation for blood pressure. + de.averbis.textanalysis.types.health.AbstractObservation + + + systolic + Measurement of systolic blood pressure. + de.averbis.textanalysis.types.measurement.Measurement + + + diastolic + Measurement of diastolic blood pressure. + de.averbis.textanalysis.types.measurement.Measurement + + + interpretation + Interpretation of fact depending on reference values or interpretation in text. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + + + de.averbis.textanalysis.types.health.BloodPressureConcept + Concept type for blood pressure. + de.averbis.textanalysis.types.health.VitalSignConcept + + + de.averbis.textanalysis.types.health.BloodPressureIgnore + Ignore patterns for blood pressure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.BooleanQualitativeValue + Supertype for qualitative values with boolean result. + de.averbis.textanalysis.types.health.QualitativeValue + + + de.averbis.textanalysis.types.health.BreastQuadrant + Aggregating annotation for breast quadrants storing additional information. + de.averbis.extraction.types.CoreAnnotation + + + clock + The location given by a clock value. + de.averbis.textanalysis.types.health.LocationClock + + + side + The side of the quadrant. + de.averbis.textanalysis.types.health.LocationSide + + + horizontal + The horizontal orientation. + de.averbis.textanalysis.types.health.LocationHorizontal + + + vertical + The vertical orientation. + de.averbis.textanalysis.types.health.LocationVertical + + + + + de.averbis.textanalysis.types.health.BreastTopographyConcept + The concept type for topography concepts describing a part of breast. + de.averbis.textanalysis.types.health.TopographyConcept + + + concept + The referenced source concept. + de.averbis.extraction.types.Concept + + + quadrant + The referenced source quadrant. + de.averbis.textanalysis.types.health.BreastQuadrant + + + + + de.averbis.textanalysis.types.health.Candidate + Supertype for candidate annotations of a diagnosis, procedure etc. + de.averbis.extraction.types.CoreAnnotation + + + conceptID + The id of the candidate. + uima.cas.String + + + dictCanon + An optional preferred term corresponding to the given id. + uima.cas.String + + + matchedTerm + Additional information about the match. + uima.cas.String + + + approach + The approach that generated this candidate. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Chimerism + Annotation for chimerism. + de.averbis.extraction.types.CoreAnnotation + + + kind + The kind of the actual chimerism: COMPLETE or MIXED. + uima.cas.String + + + value + Numeric value of chimerism. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + date + Date of chimerism analysis. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.ChimerismIndicator + Annotation for chimerism indicators. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ClinicalSection + Section type for clinical sections. + de.averbis.extraction.types.Section + + + concept + Concept indicating actual section. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + headline + Headline annotation of actual section. + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + + + content + Content annotation of actual section. + de.averbis.textanalysis.types.health.ClinicalSectionContent + + + + + de.averbis.textanalysis.types.health.ClinicalSectionCandidate + Candidates of clinical sections. + de.averbis.extraction.types.CoreAnnotation + + + headline + Headline of actual clinical section candidate. + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + + + content + Content of actual clinical section candidate. + de.averbis.textanalysis.types.health.ClinicalSectionContent + + + + + de.averbis.textanalysis.types.health.ClinicalSectionCandidateWithoutHeadline + Candidates of clinical sections without headline. + de.averbis.textanalysis.types.health.ClinicalSectionCandidate + + + concept + Non headline concept indicating actual section. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + + + de.averbis.textanalysis.types.health.ClinicalSectionContent + Clinical section content. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ClinicalSectionHeadline + Clinical section headline. + de.averbis.extraction.types.CoreAnnotation + + + headlineConcept + Concept annotation indicating headline. + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + + + + + de.averbis.textanalysis.types.health.ClinicalSectionKeywordConcept + Concept type for clinical section keywords. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.ClinicalStatusIndicator + Indicator for a clinical status of a diagnosis. Interpretation could be e.g. ACTIVE, RESOLVED etc. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.ConceptClassification + A classification for concept annotations. + de.averbis.extraction.types.CoreAnnotation + + + label + The category of the annotation, e.g., final. + uima.cas.String + + + concept + The category of the annotation, e.g., final. + de.averbis.extraction.types.Concept + + + + + de.averbis.textanalysis.types.health.ConditioningTreatmentSection + Myeloablative conditioning treatment such as irradiation therapy or chemotherapy. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.DayTimeDoseFrequency + Details of dose frequency for a specific time of day. + de.averbis.textanalysis.types.health.DoseFrequency + + + morning + Number of drug units in the morning. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + midday + Number of drug units at midday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + evening + Number of drug units in the evening. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + atNight + Number of drug units at night or bedtime. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.DeathDate + Recorded date of patient's death. + de.averbis.extraction.types.CoreAnnotation + + + date + Patient's date of death. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.Diagnosis + The actual diagnosis containing the concept and additional information. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + laterality + The laterality of the actual diagnosis. + de.averbis.textanalysis.types.health.Laterality + + + belongsTo + Diagnosis of patient or other person (family anamnesis). Possible values include 'patient' or 'family'. + uima.cas.String + + + onsetDate + The onset date of the diagnosis. + de.averbis.textanalysis.types.temporal.Date + + + kind + The kind of the diagnosis. Possible values include 'main' or 'secondary'. + uima.cas.String + + + clinicalStatus + Clinical status of the actual diagnosis. + de.averbis.textanalysis.types.health.Status + + + verificationStatus + Verification status of the actual diagnosis. Possible values: "NEGATED" if Concept is negated. + de.averbis.textanalysis.types.health.Status + + + approach + The approach that generated this diagnosis annotation. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.DiagnosisCandidate + A diagnosis candidate for a DRG coding. + de.averbis.textanalysis.types.health.Candidate + + + belongsTo + Diagnosis candidate belongs to patient or other person (family anamnesis). Possible values include 'patient' or 'family'. + uima.cas.String + + + clinicalStatus + Clinical status of the diagnosis candidate. + de.averbis.textanalysis.types.health.Status + + + verificationStatus + Verification status of the diagnosis candidate. + de.averbis.textanalysis.types.health.Status + + + + + de.averbis.textanalysis.types.health.DiagnosisCodeConcept + Concept type for diagnoses given by their code. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.DiagnosisConcept + Concept type for diagnoses. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DiagnosisConceptCandidate + A text span that might contain a DiagnosisConcept. + de.averbis.extraction.types.CoreAnnotation + + + additionalSpans + Optional annotation not in the initial span, which can influence the coding. + uima.cas.FSArray + true + + + fragments + List of annotations in span excluding the undesired indicators (e.g. LateralityIndicator) . + uima.cas.FSArray + true + + + + + de.averbis.textanalysis.types.health.DiagnosisHistorySection + History of past illness describes the history related to their current complaints, problems, + or diagnoses. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.DiagnosisSection + History of present illness describes the history related to the reason for a given procedure. It + contains the historical details leading up to and pertaining to the patient's current complaint or + reason for seeking medical care. Because history of present illness can include past surgical history + and other procedures, the Procedure History section may be included under the History of Present + Illness section or it may stand alone as its own section. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.DiagnosisSpecialConcept + Special induced Concept type for diagnoses. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.DiagnosisStatus + Clinical status (active, resolved) or verification status (assured, negated, unknown, ...) of a diagnosis. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.DischargeDateInd + Indicator for a following discharge date. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.DischargeDiagnosisSection + Hospital discharge diagnosis describes the patient's relevant problems or diagnoses that occurred + during the hospitalization or that need to be followed after hospitalization. + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.DischargeFindingSection + Hospital discharge physical findings records a narrative description of the patient's physical findings. + de.averbis.textanalysis.types.health.FindingSection + + + de.averbis.textanalysis.types.health.DischargeMedicationSection + Hospital discharge medications defines the medications that the patient is intended to take (or stop) after + discharge. This may also include a patient's prescription history and indicate the source of the medication + list, for example, from a pharmacy system versus from the patient. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.DocumentFooterSection + Section containing document footer. + de.averbis.textanalysis.types.health.MiscClinicalSection + + + de.averbis.textanalysis.types.health.DoseFormConcept + Concept type for dose forms. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DoseFrequency + Supertype of the dose frequencies. + de.averbis.extraction.types.CoreAnnotation + + + interval + The taking interval of a medication, e.g. day, week, month etc. + uima.cas.String + + + totalCount + Total count of taken drug units per interval. + uima.cas.Double + + + totalDose + Total dose of taken drug per interval. + de.averbis.textanalysis.types.measurement.Measurement + + + regimen + Annotation of the mentioned regimen, e.g. 'three times daily' + uima.tcas.Annotation + + + concept + Optional concept that was the origin of the dose frequency. + de.averbis.extraction.types.Concept + + + + + de.averbis.textanalysis.types.health.DoseFrequencyConcept + Concept type for dose frequencies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.DoseKindIndicator + Utility type for representing specific Dose Kinds, i.e, fractional. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized kind. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Drug + Drug with only one ingredient. + de.averbis.textanalysis.types.health.AbstractDrug + + + ingredient + The ingredient concept of the actual drug. + de.averbis.textanalysis.types.health.IngredientConcept + + + strength + Strength of the drug + de.averbis.textanalysis.types.health.Strength + + + + + de.averbis.textanalysis.types.health.ECGSection + Section containing information about ECG. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.ECOG + Annotation for ECOG. + de.averbis.textanalysis.types.health.ObservationWithStage + + + de.averbis.textanalysis.types.health.ECOGConcept + Concept type for ECOG. + de.averbis.textanalysis.types.health.StageObservationConcept + + + de.averbis.textanalysis.types.health.EchocardiographySection + Section containing information about echocardiography. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.EpicrisisSection + An evaluation (also called asessment, impression or diagnoses) note represents the clinician's + conclusions and working assumptions that will guide treatment of the patient. The assessment + formulates a specific plan or set of recommendations. The assessment may be a list of specific + disease entities or a narrative block. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.EstrogenReceptor + A estrogen receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.ExtendedNumericValue + + de.averbis.textanalysis.types.numericvalue.NumericValue + + + extendedStringValue + + uima.cas.String + + + + + de.averbis.textanalysis.types.health.EyeIndicator + Indicator for eye mentioning. + de.averbis.textanalysis.types.health.LateralityIndicator + + + de.averbis.textanalysis.types.health.FamilyAnamnesisSection + History of family member diseases is a report of health information, including medical, genetic, + environmental, and lifestyle factors, pertaining to the patient and his or her genetic relatives + (living or deceased). The family history information is used to determine possible or relevant health + risk factors that may have a potential impact on the patient's healthcare risk profile. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.FamilyIndicator + Indicator for a diagnosis in the family. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.FemaleGenderIndicator + Indicator for female gender mentioning. + de.averbis.textanalysis.types.health.GenderIndicator + + + de.averbis.textanalysis.types.health.FindingSection + Section containing information about findings. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.FunctionalAngiographySection + Section containing information about the functional angiography. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.FunctionalStatusSection + Functional status assessment describes the patient's status of normal functioning at the time a care + record was created. Functional statuses include information regarding the patient relative to + ambulatory ability, mental status or competency, activities of daily living (ADLs) (i.e. bathing, + dressing, feeding, grooming), home/living situation having an effect on the health status of the + patient, ability to care for self, social activity (i.e. issues with social cognition, participation + with friends and acquaintances other than family members), occupation activity (i.e. activities partly + or directly related to working), housework or volunteering, family and home responsibilities or + activities related to home and family, communication ability (i.e. issues with speech, writing or + cognition required for communication), and perception, including sight, hearing, taste, skin sensation, + kinesthetic sense, proprioception, or balance. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.GenderIndicator + Indicator for gender mentioning. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.GeneralConditionSection + Physical findings (of general status) describes general observations and readily observable attributes + of the patient, including affect and demeanor, apparent age compared to actual age, gender, ethnicity, + nutritional status based on appearance, body build and habitus (e.g., muscular, cachectic, obese), + developmental or other deformities, gait and mobility, personal hygiene, evidence of distress, and + voice quality and speech. + de.averbis.textanalysis.types.health.FindingSection + + + de.averbis.textanalysis.types.health.GleasonScore + The Gleason score. + de.averbis.extraction.types.CoreAnnotation + + + score + The combined score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + primary + The primary score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + secondary + The secondary score. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.health.GvHD + Annotation of a Graft-versus-Host-Disease diagnosis. + de.averbis.textanalysis.types.health.Diagnosis + + + continuanceStatus + GvHD status, i.e. acute, chronic. + de.averbis.textanalysis.types.health.GvHDContinuanceStatus + + + grade + Grade of the GvHD diagnosis, i.e. I, II, III, IV. + de.averbis.textanalysis.types.health.GvHDGrade + + + stage + Stage of the GvHD diagnosis, i.e. 1, 2, 3, 4 or limited, extensive. + de.averbis.textanalysis.types.health.GvHDStage + + + organ + Organ diagnosed with GvHD, i.e. skin, liver. + de.averbis.textanalysis.types.health.GvHDOrgan + + + date + The date of the diagnosis. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.GvHDContinuanceStatus + (Temporal) Status of the GvHD diagnosis, i.e. acute, chronic. + de.averbis.textanalysis.types.health.DiagnosisStatus + + + de.averbis.textanalysis.types.health.GvHDDiagnosisConcept + Concept type for Graft-versus-Host-Disease diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + de.averbis.textanalysis.types.health.GvHDGrade + Severity grade of the GvHD diagnosis, i.e. I, II, III, IV, limited, extended. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized value of GvHD in categories, i.e. I, II, III, IV, limited, extended. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.GvHDOrgan + Organ diagnosed with GvHD, i.e. skin, liver. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized name of affected organ. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.GvHDStage + Stage of the GvHD, i.e. 1, 2, 3, 4. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Stage of GvHD in integer categories, i.e. 1, 2, 3, 4. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.HER2 + A HER2 receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.HLA + Annotation type for human leukocyte antigen. + de.averbis.textanalysis.types.health.AbstractObservation + + + male + Paternal HLA manifestation. + de.averbis.textanalysis.types.health.HLAValue + + + female + Maternal HLA manifestation. + de.averbis.textanalysis.types.health.HLAValue + + + samplingDate + Date of sampling. + de.averbis.textanalysis.types.temporal.Date + + + receiptDate + Date of receipt of sample. + de.averbis.textanalysis.types.temporal.Date + + + belongsTo + Role of the person engaged in a HLA-typed human primary cells transplantation procedure. Possible values are 'RECIPIENT' or 'DONOR'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.HLAConcept + HLA parameter concept. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.HLAValue + Manifestation of allele group, HLA-protein etc. in human leukocyte antigen. + de.averbis.extraction.types.CoreAnnotation + + + alleleGroup + Allele group of actual HLA. + uima.cas.String + + + protein + Specific protein of actual HLA. + uima.cas.String + + + synonymousDNA + Synonymous DNA substitution within the coding region. + uima.cas.String + + + noncodingRegionVariant + Differences in non-coding region. + uima.cas.String + + + expressionNote + Suffix to code changes in expression. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.High + Observation higher than normal. + de.averbis.textanalysis.types.health.Abnormal + + + de.averbis.textanalysis.types.health.Hospitalisation + Hospitalisation of a patient. + de.averbis.extraction.types.CoreAnnotation + + + admissionDate + Date of admission to hospital. + de.averbis.textanalysis.types.temporal.Date + + + dischargeDate + Date of discharge from hospital. + de.averbis.textanalysis.types.temporal.Date + + + duration + Duration of stay in hospital. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.HospitalisationInd + Indicator for hospitalisation mentioning. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.IgnorePhrase + Ignore type for all kinds of medical annotations. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.IngredientConcept + Concept type for ingredients. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Irradiation + The irradiation therapy (incl. dose, kind and temporal interval). + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the irradiation. + de.averbis.textanalysis.types.health.IrradiationTherapyConcept + + + irradiationDose + The irradiation dose. + de.averbis.textanalysis.types.health.IrradiationDose + + + dateInterval + The temporal interval of the irradiation therapy. + de.averbis.textanalysis.types.temporal.DateInterval + + + + + de.averbis.textanalysis.types.health.IrradiationDose + The irradiation dose along with its distribution kind. + de.averbis.extraction.types.CoreAnnotation + + + dose + The irradiation dose measurement value. + de.averbis.textanalysis.types.measurement.Measurement + + + kind + The type of irradiation, i.e. fractional. + de.averbis.textanalysis.types.health.DoseKindIndicator + + + + + de.averbis.textanalysis.types.health.IrradiationTherapyConcept + Concept type for irradiation therapies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.LabValueIgnore + Helper type for representing text spans that should be ignored by the pattern building LaboratoryValue. + uima.tcas.Annotation + + + de.averbis.textanalysis.types.health.LaboratoryConcept + Laboratory parameter concept. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.LaboratorySection + Section containing laboratory information. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.LaboratoryValue + The actual laboratory value containing the concept and additional information. + de.averbis.textanalysis.types.health.AbstractObservation + + + fact + Measurement or numeric value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + factAssessment + A optional relative assessment of the fact. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + lowerLimit + Lower reference value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + upperLimit + Upper reference value of actual laboratory value. + de.averbis.textanalysis.types.measurement.Measurement + + + interpretation + Interpretation of fact depending on reference values or interpretation in text. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + qualitativeValue + Qualitative value of the actual laboratory value, e.g. positive, negative. + de.averbis.textanalysis.types.health.QualitativeValue + + + belongsTo + Laboratory value belongs to patient or other person. Possible values are 'RECIPIENT', 'DONOR' or 'FAMILY'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LaboratoryValueContext + An indicator annotation specifying that a nearby span is part of a lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Laterality + Laterality of an annotation, e.g. diagnosis or ophthalmology. + de.averbis.extraction.types.CoreAnnotation + + + value + Laterality value, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + reference + Indicator that determines the laterality. + de.averbis.textanalysis.types.health.LateralityIndicator + + + + + de.averbis.textanalysis.types.health.LateralityContext + Context with the same laterality. + de.averbis.extraction.types.CoreAnnotation + + + reference + Laterality of the context. + de.averbis.textanalysis.types.health.Laterality + + + + + de.averbis.textanalysis.types.health.LateralityForCodeIndicator + Indicator for the laterality of an annotation, e.g. diagnosis. Only valid if close to a ICD-10 Code. + de.averbis.extraction.types.CoreAnnotation + + + value + Value the indicator stands for, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LateralityIndicator + Indicator for the laterality of an annotation, e.g. diagnosis or ophthalmology. + de.averbis.extraction.types.CoreAnnotation + + + value + Value the indicator stands for, e.g. RIGHT, LEFT, BOTH + uima.cas.String + + + + + de.averbis.textanalysis.types.health.LeftEyeIndicator + Indicator for mentioning of left eye. + de.averbis.textanalysis.types.health.EyeIndicator + + + de.averbis.textanalysis.types.health.Limit + Limit value from text or external source. + de.averbis.textanalysis.types.measurement.Measurement + + + externalSource + Information about limit value from external source. + uima.cas.Boolean + + + + + de.averbis.textanalysis.types.health.LocationClock + The position/location given by a clock value. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationHorizontal + The position/location given by a horizontal orientation. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationSide + The location given by the side: R, L, T, U + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.LocationVertical + The position/location given by a vertical orientation. + de.averbis.textanalysis.types.health.QuadrantElement + + + de.averbis.textanalysis.types.health.Low + Observation lower than normal. + de.averbis.textanalysis.types.health.Abnormal + + + de.averbis.textanalysis.types.health.MainDiagnosisSection + Chief complaint records the patient's primary complaint (the patient's own description). + de.averbis.textanalysis.types.health.DiagnosisSection + + + de.averbis.textanalysis.types.health.MaleGenderIndicator + Indicator for male gender mentioning. + de.averbis.textanalysis.types.health.GenderIndicator + + + de.averbis.textanalysis.types.health.MedicalNegation + Annotations of medical negations. + de.averbis.extraction.types.CoreAnnotation + + + negating + List of concepts which are negated by current negation. + uima.cas.FSArray + de.averbis.extraction.types.Concept + true + + + + + de.averbis.textanalysis.types.health.MedicalPostNegation + Medical negation which negates precedent concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalPreNegation + Medical negation which negates subsequent concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalPrePostNegation + Medical negation which negates surrounding concepts. + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.MedicalSegmentNegation + Medical negation which negates self-negating concepts (e.g. tumorfrei). + de.averbis.textanalysis.types.health.MedicalNegation + + + de.averbis.textanalysis.types.health.Medication + The actual medication containing the concept and additional information. + de.averbis.extraction.types.CoreAnnotation + + + drug + Drug or multi drug of the actual medication. + de.averbis.textanalysis.types.health.AbstractDrug + + + doseForm + Dose form of the actual medication. + de.averbis.textanalysis.types.health.DoseFormConcept + + + doseFrequency + Dose frequency of the actual medication. Could be AbstractDoseFrequency or DailyDoseFrequency, WeeklyDoseFrequency etc. + de.averbis.textanalysis.types.health.DoseFrequency + + + date + Temporal information about the actual medication. + de.averbis.extraction.types.CoreAnnotation + + + administrations + The routes of administration of this medication. + uima.cas.FSArray + de.averbis.textanalysis.types.health.Administration + true + + + additionalAmounts + Additional mentions of dose amounts, e.g., 2 doses. + uima.cas.FSArray + de.averbis.textanalysis.types.health.AdditionalDoseAmount + true + + + status + Status of the medication, e.g. ADMISSION, DISCHARGE. For all available value see MedicationStatus. + de.averbis.textanalysis.types.health.MedicationStatus + + + termTypes + Additional information on clinical drug, e.g. semantic clinical drug (RxNorm Term Type). + uima.cas.FSArray + de.averbis.textanalysis.types.health.TTY + true + + + atc + The ATC Code of the medication. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.MedicationContext + An indicator annotation specifying that a nearby span is part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationHistorySection + History of medication use defines a patient's current medications and history of pertinent medications. + This term may also include a patient's prescription and dispense history. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.MedicationIgnore + Abstract super type for text spans that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationIgnoreEntity + Text spans based on a given annotation that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationIgnorePhrase + Text spans based on dictionaries or patterns that should be ignored when building the medication relation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.MedicationRecommendationSection + Recommendation for medication after discharge. + de.averbis.textanalysis.types.health.MedicationSection + + + de.averbis.textanalysis.types.health.MedicationSection + Medications administered defines medications and fluids administered during the procedure, excluding + anesthetic medications. Medications administered for anesthesia are typically documented in the + section on Anesthesia. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.MedicationStatus + Status of the medication. Available values: null, ADMISSION, ALLERGY, INPATIENT, DISCHARGE, NEGATED, CONSIDERED, INTENDED, FAMILY, CONDITIONING_TREATMENT, UNKNOWN. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.MedicationStatusIndicator + Indicator for a status of a medication. Interpretation could be e.g. NEGATED, CONSIDERED, ADMISSION, DISCHARGE. For all available value see MedicationStatus. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.MicroBiologyQualitativeValue + Qualitative values for micro biology laboratory concepts, e.g. 'Bacteria'. + de.averbis.textanalysis.types.health.QualitativeValue + + + de.averbis.textanalysis.types.health.MiscClinicalSection + Section containing other information. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ModifierIndicator + Indicator for modifiers. + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalized value of the modifier, e.g. 'WEAK'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.MorphologyClassification + A classification for morphology annotations. + de.averbis.textanalysis.types.health.ConceptClassification + + + de.averbis.textanalysis.types.health.MorphologyCodeConcept + The concept type for morphology concepts given by their codes. + de.averbis.textanalysis.types.health.MorphologyConcept + + + de.averbis.textanalysis.types.health.MorphologyConcept + The concept type for all morphology concepts. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.MorphologySpecialConcept + The concept type for morphology concepts mostly induced by some additional logic. + de.averbis.textanalysis.types.health.MorphologyConcept + + + de.averbis.textanalysis.types.health.MultiDrug + Drug with more than one ingredient. + de.averbis.textanalysis.types.health.AbstractDrug + + + drugs + List of all drugs contained in the actual multi drug + uima.cas.FSArray + de.averbis.textanalysis.types.health.Drug + true + + + concept + The original ingredient concept responsible for the multi drug. + de.averbis.textanalysis.types.health.IngredientConcept + + + + + de.averbis.textanalysis.types.health.NYHA + Annotation for NYHA. + de.averbis.textanalysis.types.health.ObservationWithStage + + + de.averbis.textanalysis.types.health.NYHAConcept + Concept type for NYHA. + de.averbis.textanalysis.types.health.StageObservationConcept + + + de.averbis.textanalysis.types.health.NegationScope + The negated scope. + de.averbis.textanalysis.types.AnnotationScope + + + de.averbis.textanalysis.types.health.Negative + Negative result of an observation (no interpretation!). + de.averbis.textanalysis.types.health.BooleanQualitativeValue + + + de.averbis.textanalysis.types.health.NoDiagnosis + An indicator annotation specifying that this span is no part of a diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoDiagnosisContext + An indicator annotation specifying that a nearby span is no part of a diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoDiagnosisContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValue + An indicator annotation specifying that this span is no part of a laboratory value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValueContext + An indicator annotation specifying that a nearby span is no part of a lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoLaboratoryValueContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the lab value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedication + An indicator annotation specifying that this span is no part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedicationContext + An indicator annotation specifying that a nearby span is no part of a medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoMedicationContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the medication. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedure + An indicator annotation specifying that this span is no part of a procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedureContext + An indicator annotation specifying that a nearby span is no part of a procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoProcedureContextBlocker + An indicator annotation specifying that a nearby context is applicable for changing the semantic of the procedure. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.NoQualitativeValue + An indicator annotation specifying that a span is not an qualitative value. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.Normal + Normal observation. + de.averbis.textanalysis.types.health.AbstractInterpretation + + + de.averbis.textanalysis.types.health.ObservationSection + The Procedure findings section records clinically significant observations confirmed or discovered + during a procedure, treatment or service. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ObservationStage + Stage of the observation, i.e. Stage I, II, 1, 2. + de.averbis.extraction.types.CoreAnnotation + + + normalizedValue + Normalized value of the stage. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.ObservationStageIndicator + Indicator for observation stages, i.e. Stage, status, class etc. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.health.ObservationWithStage + Annotation for observation with stage, i.e. NYHA I, ECOG 3. + de.averbis.textanalysis.types.health.AbstractObservation + + + stage + Observation stage. + de.averbis.textanalysis.types.health.ObservationStage + + + + + de.averbis.textanalysis.types.health.OcularFundusSection + Section containing information about the ocular fundus. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.Ophthalmology + Main type for ophthalmological terms. + de.averbis.textanalysis.types.health.AbstractObservation + + + laterality + Laterality of the ophthalmological term. + de.averbis.textanalysis.types.health.Laterality + + + + + de.averbis.textanalysis.types.health.OphthalmologyConcept + Concept type for ophthalmological terms. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.OphthalmologySection + Section containing information about ophthalmology. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.OpticalCoherenceTomographySection + Section containing information about the optical coherence tomography. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.OrganismConcept + Organism concepts, e.g. Bacteria. + de.averbis.extraction.types.Concept + + + kind + The kind of the OrganismConcept, e.g. 'Bacterium', 'Virus' or 'Fungus' + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Organization + Organization name annotation which stores (optionally) its type and correspondence (e.g. sender, receiver). + de.averbis.extraction.types.CoreAnnotation + + + organizationType + The kind/type of organization (e.g. rehabilitation). + uima.cas.String + + + correspondence + The correspondence type (e.g. sender, receiver). + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PathologyDocumentClassification + A classification for a single pathology document for specific elements and code like + diagnosis. + de.averbis.extraction.types.CoreAnnotation + + + category + The category of the document, e.g., MAMMA. + uima.cas.String + + + diagnosis + The code of the relevant diagnosis. + uima.cas.String + + + topography + The code of the relevant topography. + uima.cas.String + + + morphology + The code of the relevant morphology. + uima.cas.String + + + tumor + The TNM code of the relevant tumor. + uima.cas.String + + + node + The TNM code of the relevant node. + uima.cas.String + + + metastasis + The TNM code of the relevant metastasis. + uima.cas.String + + + grading + The relevant grading. + uima.cas.String + + + location + The relevant location. + uima.cas.String + + + rClass + The relevant R-classification. + uima.cas.String + + + side + The relevant side, e.g., L, R, T. + uima.cas.String + + + lymphnodesAffected + The amount of affected lymph nodes. + uima.cas.Integer + + + lymphnodesTested + The amount of tested lymph nodes. + uima.cas.Integer + + + sentinelLymphnodesAffected + The amount of affected sentinel lymph nodes. + uima.cas.Integer + + + sentinelLymphnodesTested + The amount of tested sentinel lymph nodes. + uima.cas.Integer + + + thickness + The thickness of the skin tumor. + uima.cas.Double + + + lymphaticInvasion + The invasion of the cancer to the lymphatic system. + uima.cas.String + + + vascularInvasion + The invasion of the cancer to the vascular system. + uima.cas.String + + + perineuralInvasion + The invasion of the cancer to the space surrounding a nerve. + uima.cas.String + + + resultDate + The date of the result/findings. + uima.cas.String + + + scores + List of different scores, e.g. GleasonScore. + uima.cas.FSArray + de.averbis.extraction.types.CoreAnnotation + true + + + categoryAnnotation + Optional annotation representing the category of the document. + de.averbis.extraction.types.Category + + + diagnosisConcept + Optional annotation representing the relevant diagnosis. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + topographyConcept + Optional annotation representing the relevant topography. + de.averbis.textanalysis.types.health.TopographyConcept + + + morphologyConcept + Optional annotation representing the relevant morphology. + de.averbis.textanalysis.types.health.MorphologyConcept + + + tumorAnnotation + Optional annotation representing the relevant tumor. + de.averbis.textanalysis.types.health.TNMTumor + + + nodeAnnotation + Optional annotation representing the relevant node. + de.averbis.textanalysis.types.health.TNMNode + + + metastasisAnnotation + Optional annotation representing the relevant metastasis. + de.averbis.textanalysis.types.health.TNMMetastasis + + + gradingAnnotation + Optional annotation representing the relevant grading. + de.averbis.textanalysis.types.health.TNMGrading + + + locationAnnotation + Optional annotation representing the relevant location. + de.averbis.textanalysis.types.health.TNMLocation + + + rClassAnnotation + Optional annotation representing the relevant R-classification. + de.averbis.textanalysis.types.health.TNMRClass + + + sideAnnotation + Optional annotation representing the relevant side. + de.averbis.textanalysis.types.health.LocationSide + + + lymphnodesAnnotation + Optional annotation representing the lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodes + + + sentinelLymphnodesAnnotation + Optional annotation representing the sentinel lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + + + thicknessAnnotation + Optional annotation representing the thickness of the skin tumor. + de.averbis.textanalysis.types.health.LaboratoryValue + + + lymphaticInvasionAnnotation + Optional annotation representing the invasion of the cancer to the lymphatic + system. + de.averbis.textanalysis.types.health.TNMAdditional + + + vascularInvasionAnnotation + Optional annotation representing the invasion of the cancer to the vascular + system. + de.averbis.textanalysis.types.health.TNMAdditional + + + perineuralInvasionAnnotation + Optional annotation representing the invasion of the cancer to the space + surrounding a nerve. + de.averbis.textanalysis.types.health.TNMAdditional + + + resultDateAnnotation + Optional annotation representing the date of the findings/result. + de.averbis.textanalysis.types.health.ResultDate + + + + + de.averbis.textanalysis.types.health.PatientContactIndicator + Indicator for a mentioning of a person not related to the patient. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.PatientGender + The gender of the patient. + de.averbis.extraction.types.CoreAnnotation + + + value + Patient's gender value, i.e. female/male. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PatientGroupIndicator + Indicator for a mentioning of a person in the patient's context. + de.averbis.textanalysis.types.health.PersonGroupIndicator + + + de.averbis.textanalysis.types.health.PatientIndicator + Indicator for a mentioning of the patient. + de.averbis.textanalysis.types.health.PatientGroupIndicator + + + de.averbis.textanalysis.types.health.PatientInformation + Patient information. + de.averbis.extraction.types.CoreAnnotation + + + deathDate + Patient's date of death. + de.averbis.textanalysis.types.health.DeathDate + + + deceased + Patient deceased. + uima.cas.Boolean + + + gender + Patient's gender. + de.averbis.textanalysis.types.health.PatientGender + + + name + Patient's name. + de.averbis.textanalysis.types.health.PatientName + + + + + de.averbis.textanalysis.types.health.PatientName + The patient's name. + de.averbis.textanalysis.types.PersonName + + + de.averbis.textanalysis.types.health.PatientNameConcept + Concept with the patient's full name. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.PersonGroupIndicator + Indicator for the mentioning of a person. + de.averbis.extraction.types.CoreAnnotation + + + value + Description of the person group, e.g. "FAMILY" or "OTHER" + uima.cas.String + + + + + de.averbis.textanalysis.types.health.PhysicalTherapy + []. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the physical therapy. + de.averbis.textanalysis.types.health.PhysicalTherapyConcept + + + status + The status of the physical therapy. + de.averbis.textanalysis.types.health.PhysicalTherapyStatus + + + + + de.averbis.textanalysis.types.health.PhysicalTherapyConcept + Concept type for physical therapies. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.PhysicalTherapyStatus + Status of physical therapies. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.PhysicalTherapyStatusIndicator + Indicator for status of physical therapy. Interpretation could be e.g. NEGATED, HISTORY, or PLANNED. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.Positive + Positive result of an observation (no interpretation!). + de.averbis.textanalysis.types.health.BooleanQualitativeValue + + + de.averbis.textanalysis.types.health.PriorLabValueIndicator + Helper type for representing text spans that indicating a prior LaboratoryValue. + uima.tcas.Annotation + + + de.averbis.textanalysis.types.health.PriorLaboratoryValue + A prior LaboratoryValue. + de.averbis.textanalysis.types.health.LaboratoryValue + + + de.averbis.textanalysis.types.health.Procedure + The procedure annotation. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the procedure. + de.averbis.textanalysis.types.health.ProcedureConcept + + + laterality + Laterality of the procedure, i.e. NULL (default), RIGHT, LEFT, BOTH. + de.averbis.textanalysis.types.health.Laterality + + + status + Procedure status feature, i.e. HISTORY, PLANNED, NEGATED. + de.averbis.textanalysis.types.health.ProcedureStatus + + + date + Temporal information about the actual procedure. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.ProcedureCandidate + A procedure candidate for a OPS coding. + de.averbis.textanalysis.types.health.Candidate + + + de.averbis.textanalysis.types.health.ProcedureConcept + Concept type for procedures. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.ProcedureHistorySection + This section defines all interventional, surgical, diagnostic, or therapeutic procedures or treatments + pertinent to the patient historically and at the time the document is generated. + de.averbis.textanalysis.types.health.ProcedureSection + + + de.averbis.textanalysis.types.health.ProcedureSection + Procedure records the descriptions of the procedure with an extensive narrative and may include + procedure site preparation, pertinent details related to measurements and markings, procedure times, + instrumentation, and vital signs and other monitoring data. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.ProcedureStatus + Annotation type for procedure status, i.e. HISTORY, PLANNED, NEGATED. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.ProcedureStatusIndicator + Indicator for status of procedure. Interpretation could be e.g. NEGATED, CANCELED, COMNPLETED or PLANNED. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.ProgesteroneReceptor + A progesterone receptor providing a status and percentage. + de.averbis.textanalysis.types.health.Receptor + + + de.averbis.textanalysis.types.health.QuadrantElement + Abstract type for element of a quadrant. + de.averbis.extraction.types.CoreAnnotation + + + kind + Label storing the type of indicator, e.g., VERTICAL or SIDE. + uima.cas.String + + + element + The value of the indicator annotation, e.g., BOTTOM or R + uima.cas.String + + + + + de.averbis.textanalysis.types.health.QualitativeValue + Supertype for qualitative values. + de.averbis.extraction.types.CoreAnnotation + + + value + Value of the qualitative value, e.g. 'UNKNOWN', 'ABNORMAL', 'STAINING', 'POSITIVE', 'NEGATIVE'. + uima.cas.String + + + modifier + Modifier for the qualitative value's value, e.g. 'WEAK', 'MODERATE', 'STRONG'. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Receptor + A generic receptor providing a status and percentage. + de.averbis.extraction.types.CoreAnnotation + + + status + The status with an interpretation, e.g., "++"". + de.averbis.textanalysis.types.health.ReceptorStatus + + + percentage + The percentage represented as a measurement. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.ReceptorStatus + The status of a receptor. + de.averbis.textanalysis.types.health.Status + + + de.averbis.textanalysis.types.health.Refraction + + de.averbis.extraction.types.CoreAnnotation + + + sphere + + de.averbis.textanalysis.types.health.VANumericValue + + + cylinder + + de.averbis.textanalysis.types.health.VANumericValue + + + axis + + de.averbis.textanalysis.types.health.VANumericValue + + + + + de.averbis.textanalysis.types.health.RelevantVisualAcuity + Best or actual visual acuity, selected from multiple VisualAcuity- or VisualAcuityValues. + de.averbis.textanalysis.types.health.VisualAcuity + + + de.averbis.textanalysis.types.health.RemovedAnnotation + A reference to the annotation that was removed. + de.averbis.extraction.types.CoreAnnotation + + + removed + Annotation that has been removed. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.health.RemovedDiagnosis + A reference to the diagnosis that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedDiagnosisConcept + A reference to the diagnosis concept that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedLaboratoryValue + A reference to the laboratory value that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedMedication + A reference to the medication that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.RemovedObservation + A reference to the observation that was removed. + de.averbis.textanalysis.types.health.RemovedAnnotation + + + de.averbis.textanalysis.types.health.ResultDate + The date of the result/findings. + de.averbis.extraction.types.CoreAnnotation + + + date + Date annotation holding the normalized value. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.health.RightEyeIndicator + Indicator for mentioning of right eye. + de.averbis.textanalysis.types.health.EyeIndicator + + + de.averbis.textanalysis.types.health.SocialAnamnesisSection + The Social history section contains data defining the patient's occupational, personal (e.g. lifestyle), + social, and environmental history and health risk factors, as well as administrative data such as + marital status, race, ethnicity and religious affiliation. + de.averbis.textanalysis.types.health.AnamnesisSection + + + de.averbis.textanalysis.types.health.SonographySection + Section containing information about sonography. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.SpecialistDepartment + Specialist department with additional information e.g. about department type. + de.averbis.extraction.types.CoreAnnotation + + + concept + The actual concept of the specialist department. + de.averbis.textanalysis.types.health.SpecialistDepartmentConcept + + + departmentType + Type of the department, e.g. sender. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.SpecialistDepartmentConcept + Concept type for specialist department. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Specimen + Specimen procedure information type. + de.averbis.extraction.types.CoreAnnotation + + + identifier + Identifier of this specimen. + uima.cas.String + + + diagnosis + The diagnosis of the specimen. + de.averbis.textanalysis.types.health.DiagnosisConcept + + + morphology + The morphology of the specimen. + de.averbis.textanalysis.types.health.MorphologyConcept + + + topography + The topography of the specimen. + de.averbis.textanalysis.types.health.TopographyConcept + + + laterality + Optional laterality. + de.averbis.textanalysis.types.health.Laterality + + + descriptions + Additional descriptions of the specimen. + uima.cas.FSArray + de.averbis.textanalysis.types.health.Specimen + true + + + + + de.averbis.textanalysis.types.health.SpecimenSection + The Procedure specimens taken section records the tissues, objects, or samples taken from the patient + during the procedure including biopsies, aspiration fluid, or other samples sent for pathological + analysis. The narrative may include a description of the specimens. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.StageObservationConcept + Concept type for observation stage. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.Status + Supertype for status annotations of a diagnosis, medication etc. + de.averbis.extraction.types.CoreAnnotation + + + interpretation + Interpretation of referenced value. + uima.cas.String + + + statusReference + Reference to annotation that specifies/ verifies status. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.health.StatusIndicator + Indicator for a status of a diagnosis, medication etc.. + de.averbis.extraction.types.CoreAnnotation + + + interpretation + Interpretation of referenced value, e.g. ASSURED, NEGATED, SUSPECTED etc. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Strength + The strength of a drug concerning a medication. + de.averbis.extraction.types.CoreAnnotation + + + concept + An optional concept describing the strength. + de.averbis.textanalysis.types.health.StrengthConcept + + + measurement + The actual strength as a measurement + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.StrengthConcept + Concept type for strengths. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.SymptomSection + The Review of systems section contains a relevant collection of symptoms and functions systematically + gathered by a clinician. It includes symptoms the patient is currently experiencing, some of which + were not elicited during the history of present illness, as well as a potentially large number of + pertinent negatives, for example, symptoms that the patient denied experiencing. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.TNMAdditional + Additional TNM mentions + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMBasic + The basic type of a TNM mention providing a value feature. + de.averbis.extraction.types.CoreAnnotation + + + value + The value of the TNM mention. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TNMCertainty + The C-factor, or certainty factor, reflects the validity of classification according + to the diagnostic methods employed. Its use is optional. The C-factor definitions are: + C1: Evidence from standard diagnostic means (e.g., inspection, palpation, and standard radiography, + intraluminal endoscopy for tumors of certain organs). C2: Evidence obtained by special + diagnostic means (e.g., radiographic imaging in special projections, tomography, computerized + tomography [CT], ultrasonography, lymphography, angiography, scintigraphy, magnetic resonance + imaging [MRI], endoscopy, biopsy, and cytology). C3: Evidence from surgical exploration, + including biopsy and cytology. C4: Evidence of the extent of disease following definitive + surgery and pathological examination of the resected specimen. C5: Evidence from autopsy + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMDocumentClassification + The TNM classification result for a document. + de.averbis.extraction.types.CoreAnnotation + + + tumor + tumor + de.averbis.textanalysis.types.health.TNMTumor + + + node + node + de.averbis.textanalysis.types.health.TNMNode + + + metastasis + metastasis + de.averbis.textanalysis.types.health.TNMMetastasis + + + grading + grading + de.averbis.textanalysis.types.health.TNMGrading + + + location + location + de.averbis.textanalysis.types.health.TNMLocation + + + rClass + rClass + de.averbis.textanalysis.types.health.TNMRClass + + + certainty + certainty + de.averbis.textanalysis.types.health.TNMCertainty + + + lymphaticInvasion + lymphaticInvasion + de.averbis.textanalysis.types.health.TNMLymphaticInvasion + + + vascularInvasion + vascularInvasion + de.averbis.textanalysis.types.health.TNMVascularInvasion + + + perineuralInvasion + perineuralInvasion + de.averbis.textanalysis.types.health.TNMPerineuralInvasion + + + additional + additional + de.averbis.textanalysis.types.health.TNMAdditional + + + + + de.averbis.textanalysis.types.health.TNMElement + Abstract type for a TNM element with modifiers. + de.averbis.textanalysis.types.health.TNMEntity + + + modifiers + The prefix modifiers of the element. + uima.cas.FSArray + de.averbis.textanalysis.types.health.TNMModifier + true + + + postModifier + The postfix modifier of the element. + de.averbis.textanalysis.types.health.TNMPostModifier + + + + + de.averbis.textanalysis.types.health.TNMEntity + Abstract type for a TNM entity providing a label. + de.averbis.textanalysis.types.health.TNMBasic + + + label + Label of the entity describing the type of the entity, e.g., TUMOR or GRADING. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TNMGrading + G (1–4): the grade of the cancer cells (i.e. they are "G1" if they are good + differentiated to normal cells, and "G3" if they appear poorly differentiated); + Low grade = Well-differentiated = Grade 1; + Intermediate grade = Moderately differentiated = Grade 2; + High grade = Poorly differentiated = Grade 3; + Undifferentiated = Anaplastic = Grade 4 + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMLocation + Further specification of the metastasis: Pulmonary (PUL), Bone marrow (MAR), Osseous + (OSS), Pleura (PLE), Hepatic (HEP), + Peritoneum (PER), Brain (BRA), Adrenals (ADR), Lymph nodes (LYM), Skin (SKI), Others (OTH) + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMLymphNodes + Information about the attacked and tested lymph nodes. + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + + + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + Information about the attacked and tested sentinel lymph nodes. + de.averbis.textanalysis.types.health.AbstractTNMLymphNodes + + + de.averbis.textanalysis.types.health.TNMLymphaticInvasion + Information about the lymphatic invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TNMMetastasis + M: presence of distant metastasis. Mx: metastasis cannot be evaluated. M0: no + distant metastasis. M1: metastasis to distant organs (beyond regional lymph nodes). + de.averbis.textanalysis.types.health.TNMElement + + + de.averbis.textanalysis.types.health.TNMModifier + A modifier of a TNM element + de.averbis.textanalysis.types.health.TNMBasic + + + de.averbis.textanalysis.types.health.TNMNode + N: degree of spread to regional lymph nodes. Examples: Nx: lymph nodes cannot be + evaluated. N0: tumor cells absent from regional lymph nodes. N1: regional lymph node metastasis + present; (at some sites: tumor spread to closest or small number of regional lymph nodes). N2: + tumor spread to an extent between N1 and N3 (N2 is not used at all sites). N3: tumor spread to + more distant or numerous regional lymph nodes (N3 is not used at all sites). + de.averbis.textanalysis.types.health.TNMElement + + + lymphNodes + The attacked and tested lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodes + + + lymphNodesSentinel + The attacked and tested sentinel lymph nodes. + de.averbis.textanalysis.types.health.TNMLymphNodesSentinel + + + + + de.averbis.textanalysis.types.health.TNMNotation + The aggregating annotation for TNM annotations. + de.averbis.textanalysis.types.health.TNMBasic + + + tumor + The tumor annotations. + uima.cas.FSArray + true + + + node + The node annotations. + uima.cas.FSArray + true + + + metastasis + The metastasis annotations. + uima.cas.FSArray + true + + + grading + The grading annotations + uima.cas.FSArray + true + + + location + The location annotations + uima.cas.FSArray + true + + + rClass + The R class annotations + uima.cas.FSArray + true + + + certainty + The certainty annotations + uima.cas.FSArray + true + + + additional + The additional annotations + uima.cas.FSArray + true + + + + + de.averbis.textanalysis.types.health.TNMPerineuralInvasion + Information about the perineural invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TNMPostModifier + Postmodifier of an element: a, b, c. Among others subclassification of tumor size, + e.g. T1a: tumor under 0.1cm + de.averbis.textanalysis.types.health.TNMBasic + + + de.averbis.textanalysis.types.health.TNMRClass + Residual Tumor (R) Classification. Rx: Presence of residual tumor cannot be + assessed. R0: No residual tumor. R1: Microscopic residual tumor. R2: Macroscopic residual + tumor + de.averbis.textanalysis.types.health.TNMEntity + + + de.averbis.textanalysis.types.health.TNMTumor + T: size or direct extent of the primary tumor. Examples: Tx: tumor cannot be + evaluated. + Tis: carcinoma in situ. T0: no signs of tumor. T1, T2, T3, T4: size and/or extension of the primary + tumor. + de.averbis.textanalysis.types.health.TNMElement + + + de.averbis.textanalysis.types.health.TNMVascularInvasion + Information about the vascular invasion. + de.averbis.textanalysis.types.health.TNMAdditional + + + de.averbis.textanalysis.types.health.TTY + RxNorm Term Type + de.averbis.extraction.types.CoreAnnotation + + + kind + Kind of term type, e.g. SCD. + uima.cas.String + + + code + Term type code for actual medication. + uima.cas.String + + + description + Term type description for actual medication. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.Tensio + Annotation for Tensio. + de.averbis.textanalysis.types.health.AbstractObservation + + + leftEye + Tensio measurement of left eye. + de.averbis.textanalysis.types.measurement.Measurement + + + rightEye + Tensio measurement for right eye. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.health.TensioConcept + Concept type for tensio. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.TensioSection + Section containing information about the tensio. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.TherapySection + This term was originally created for, though not limited in use to, the HL7 Implementation Guide for + CDA: Progress Note. The Interventions section contains information about the specific interventions + provided during the healthcare visit. Depending on the type of intervention(s) provided (procedural, + education, application of assistive equipment, etc.), the details will vary but may include specification + of frequency, intensity, and duration. + de.averbis.textanalysis.types.health.ClinicalSection + + + de.averbis.textanalysis.types.health.TimeMeasurementDoseFrequency + Details of dose frequency with interval given by a time measurement like daily or each two weeks. + de.averbis.textanalysis.types.health.DoseFrequency + + + de.averbis.textanalysis.types.health.TopographyClassification + A classification for topography annotations. + de.averbis.textanalysis.types.health.ConceptClassification + + + de.averbis.textanalysis.types.health.TopographyCodeConcept + The concept type for topography concepts given by their code. + de.averbis.textanalysis.types.health.TopographyConcept + + + de.averbis.textanalysis.types.health.TopographyConcept + The concept type for all topography concepts. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.TopographySpecialConcept + The concept type for special topography concepts mostly induced by some additional logic. + de.averbis.textanalysis.types.health.TopographyConcept + + + de.averbis.textanalysis.types.health.TransplantationRoleIndicator + An indicator annotation specifying the role of a person, e.g. recipient/donor. + de.averbis.extraction.types.CoreAnnotation + + + role + The role of a person. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.TreatmentRecommendationSection + Plan of care notes (previously defined as "Plan of treatment") contains data that defines pending + orders, interventions, encounters, services, and procedures for the patient. The plan includes + prospective, unfulfilled, or incomplete orders and requests only. The plan may also contain + information about ongoing care of the patient and information regarding goals and clinical reminders. + de.averbis.textanalysis.types.health.TherapySection + + + de.averbis.textanalysis.types.health.TumorStage + Stage information describing a tumor mention. + de.averbis.extraction.types.CoreAnnotation + + + stage + The stage of the tumor. + de.averbis.textanalysis.types.health.TumorStageIndicator + + + modifier + Modifier of the tumor stage. + de.averbis.textanalysis.types.health.TumorStageModifierIndicator + + + + + de.averbis.textanalysis.types.health.TumorStageIndicator + Indicator for a tumor stage representing a numeric value. + de.averbis.extraction.types.CoreAnnotation + + + value + Numeric value of the stage. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.health.TumorStageModifierIndicator + Indicator for a tumor stage modifier. + de.averbis.extraction.types.CoreAnnotation + + + value + Value of the tumor stage modifier indicator. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VANumericValue + Numeric values in context of visual acuity. + de.averbis.extraction.types.CoreAnnotation + + + value + Numeric value. + uima.cas.Double + + + + + de.averbis.textanalysis.types.health.VerificationStatusIndicator + Indicator for a verification status of a diagnosis. Interpretation could be e.g. ASSURED, NEGATED, SUSPECTED etc. + de.averbis.textanalysis.types.health.StatusIndicator + + + de.averbis.textanalysis.types.health.VisualAcuity + Complex type of visual acuity observation. + de.averbis.textanalysis.types.health.AbstractObservation + + + leftEye + Left eye's visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityValue + + + rightEye + Right eye's visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityValue + + + + + de.averbis.textanalysis.types.health.VisualAcuityAdditionalInformation + + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalization of kind of comment, e.g. "AR_NOT_POSSIBLE" for "AR nicht moeglich", "DOES_NOT_IMPROVE" for "AR bessert nicht". + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuityConcept + Concept type for visual acuity. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.VisualAcuityCorrection + + de.averbis.extraction.types.CoreAnnotation + + + normalized + Normalization of visual acuity correction, e.g. "CC" for cum correctione, "AR" for auto refraction. + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuityFact + + de.averbis.textanalysis.types.health.VANumericValue + + + normalizedString + Normalization of visual acuity value, e.g. "NLP" for no light perception, "1/20" for "1/20p". + uima.cas.String + + + + + de.averbis.textanalysis.types.health.VisualAcuitySection + Section containing information about the visual acuity. + de.averbis.textanalysis.types.health.OphthalmologySection + + + de.averbis.textanalysis.types.health.VisualAcuityValue + Visual acuity of one eye. + de.averbis.extraction.types.CoreAnnotation + + + fact + Value of the visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityFact + + + meter + Visual acuity measured with blackboard. + uima.cas.Boolean + + + correction + Correction during measuring visual acuity. + de.averbis.textanalysis.types.health.VisualAcuityCorrection + + + refraction + The measured refraction. + de.averbis.textanalysis.types.health.Refraction + + + pinHole + Visual acuity measured with pin hole. + uima.cas.Boolean + + + additionalInformation + Kind of comment, e.g. "AR_NOT_POSSIBLE", "DOES_NOT_IMPROVE". + de.averbis.textanalysis.types.health.VisualAcuityAdditionalInformation + + + + + de.averbis.textanalysis.types.health.VitalSignConcept + Concept type for vital sign. + de.averbis.extraction.types.Concept + + + de.averbis.textanalysis.types.health.VitalSignSection + Section containing information about vital signs. + de.averbis.textanalysis.types.health.ObservationSection + + + de.averbis.textanalysis.types.health.WeekDayDoseFrequency + Details of dose frequency for a specific weekday. + de.averbis.textanalysis.types.health.DoseFrequency + + + monday + Number of drug units on monday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + tuesday + Number of drug units on tuesday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + wednesday + Number of drug units on wednesday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + thursday + Number of drug units on thursday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + friday + Number of drug units on friday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + saturday + Number of drug units on saturday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + sunday + Number of drug units on sunday. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.measurement.ComparisonIndicator + A textual representation of a comparison like '<=' or 'unter', also able to + indicate an interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.DictionaryMeasurementMention + A textual representation indicating a measurement. This is a helper type for + measurements that combine numeric values and units or cause other problems for the unit parsing. + de.averbis.extraction.types.CoreAnnotation + + + value + Parseable value of the measurement. + uima.cas.String + + + unit + Parseable unit of the measurement. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.GreaterIndicator + A textual representation indicating something is 'greater', also able to indicate an + interval. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + de.averbis.textanalysis.types.measurement.IntervalIndicator + A textual representation indicating something an interval like '-' or 'bis' + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.LessIndicator + A textual representation indicating something is 'less', also able to indicate an + interval. + de.averbis.textanalysis.types.measurement.ComparisonIndicator + + + de.averbis.textanalysis.types.measurement.Measurement + A measurement combining a numeric value and a unit. + de.averbis.extraction.types.CoreAnnotation + + + unit + The unit of the measurement. + de.averbis.textanalysis.types.measurement.Unit + + + value + The numeric value of the measurement. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + normalizedUnit + Normalized string value of the unit. + uima.cas.String + + + normalizedAsciiUnit + Ascii normalized string value of the unit. + uima.cas.String + + + normalizedValue + The normalized value of the measurement. + This value is the result of the transformation of the numeric value according to the + transformation of the unit to its standard unit. + uima.cas.Double + + + normalized + The concatenation of the normalized numeric value and the ascii normalized unit. + uima.cas.String + + + parsedUnit + Optional parsable unit string which replaces the unit annotation. It is utilized + for normalization. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.MeasurementInterval + An interval defined by two measurements, a low and high limit. + de.averbis.extraction.types.CoreAnnotation + + + low + The lower bound of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + high + The upper bound of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + lowExcluded + Marker set to true if the lower bound itself is not part of the interval. + uima.cas.Boolean + + + highExcluded + Marker set to true if the upper bound itself is not part of the interval. + uima.cas.Boolean + + + + + de.averbis.textanalysis.types.measurement.NoUnit + A textual position that is not a unit. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.measurement.RelativeMeasurementInterval + A relative interval defined by two measurements, a base and deflection. + de.averbis.textanalysis.types.measurement.MeasurementInterval + + + base + The base of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + deflection + The deflection of the interval. + de.averbis.textanalysis.types.measurement.Measurement + + + + + de.averbis.textanalysis.types.measurement.SimpleMeasurementInterval + An interval extending MeasurementInterval with several primitive features + representing two measurements. + de.averbis.textanalysis.types.measurement.MeasurementInterval + + + lowNormalizedUnit + The normalized unit of the lower bound. + uima.cas.String + + + lowNormalizedValue + The normalized value of the lower bound. + uima.cas.Double + + + lowNormalized + The normalized value combined with the normalized unit of the lower bound. + uima.cas.String + + + lowParsedUnit + The parsed unit of the lower bound. + uima.cas.String + + + highNormalizedUnit + The normalized unit of the upper bound. + uima.cas.String + + + highNormalizedValue + The normalized value of the upper bound. + uima.cas.Double + + + highNormalized + The normalized value combined with the normalized unit of the upper bound. + uima.cas.String + + + highParsedUnit + The parsed unit of the upper bound. + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.Unit + + de.averbis.extraction.types.CoreAnnotation + + + normalizedAscii + Ascii normalized string value of the unit. + uima.cas.String + + + parsed + String value of the parsed/identified unit. + uima.cas.String + + + normalized + Normalized string value of the unit. + uima.cas.String + + + dimension + The dimension of the unit in the form like '[L]^3' for volume + uima.cas.String + + + + + de.averbis.textanalysis.types.measurement.UnitParseAnchor + Helper type to use as anchor for unit parsing. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.numericvalue.ConjunctionFragment + A text span indicating a conjunction of numbers, which may also be located within + token like in 'fünfundzwanzig' + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.numericvalue.Fraction + A fraction of two NumericValue annotations. + de.averbis.extraction.types.CoreAnnotation + + + numerator + The numerator of the fraction. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + denominator + The denominator of the fraction. + de.averbis.textanalysis.types.numericvalue.NumericValue + + + + + de.averbis.textanalysis.types.numericvalue.LanguageContainer + A container annotation specifying the language of the covered text. + de.averbis.extraction.types.CoreAnnotation + + + language + The language locale like 'de' or 'en'. + uima.cas.String + + + + + de.averbis.textanalysis.types.numericvalue.NumericValue + Represents a text span which can be interpreted as a numeric value which is stored + in a feature. + de.averbis.extraction.types.CoreAnnotation + + + value + The actual double value of the numeric value. + uima.cas.Double + + + + + de.averbis.textanalysis.types.numericvalue.RomanNumeral + Annotation for roman numerals. + de.averbis.extraction.types.CoreAnnotation + + + value + Integer value of the roman numeral. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.numericvalue.SimpleFraction + A fraction of two integer values. + de.averbis.extraction.types.CoreAnnotation + + + numerator + The numerator of the fraction. + uima.cas.Integer + + + denominator + The denominator of the fraction. + uima.cas.Integer + + + + + de.averbis.textanalysis.types.temporal.Date + The expression describes a calendar time. + de.averbis.textanalysis.types.temporal.Timex3 + + + day + The day of the actual date. + uima.tcas.Annotation + + + month + The month of the actual date. + uima.tcas.Annotation + + + year + The year of the actual date. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.temporal.DateInterval + The expression describes an interval(or set) of dates defined + by the start and end date of an event. + de.averbis.textanalysis.types.temporal.TemporalSet + + + startDate + The start date of the temporal interval. + de.averbis.textanalysis.types.temporal.Date + + + endDate + The end date of the temporal interval. + de.averbis.textanalysis.types.temporal.Date + + + + + de.averbis.textanalysis.types.temporal.DayTime + Annotation indicating a time of day e.g., 'in the + morning'. + uima.tcas.Annotation + + + timeOfDay + Number specifying the time of the day. + uima.cas.String + + + + + de.averbis.textanalysis.types.temporal.DocumentDate + Annotation representing the date and time presenting the + document if available, e.g., + the creation time. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.Duration + The expression describes a duration. This value is + assigned to explicit durations. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.TemporalIntervalBeginIndicator + Indicator for a possible begin of a temporal interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.temporal.TemporalIntervalEndIndicator + Indicator for a possible end of a temporal interval. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.temporal.TemporalSet + The expression describes a set of times. + de.averbis.textanalysis.types.temporal.Timex3 + + + de.averbis.textanalysis.types.temporal.Time + The expression refers to a time of the day, even if in a + very indefinite way. + de.averbis.textanalysis.types.temporal.Timex3 + + + hour + The hour of the actual time. + uima.tcas.Annotation + + + minute + The minute of the actual time. + uima.tcas.Annotation + + + second + The second of the actual time. + uima.tcas.Annotation + + + + + de.averbis.textanalysis.types.temporal.Timex3 + Represents a text span which can be interpreted as a + numeric value which is stored in + a feature. + de.averbis.extraction.types.CoreAnnotation + + + tid + Non-optional attribute. Each TIMEX3 expression has to + be identified by a unique ID + number. This is automatically + assigned by the annotation tool. + uima.cas.String + + + kind + Non-optional attribute. Each TIMEX3 is assigned one of + the following types: DATE, + TIME, DURATION, or SET. The format of + the value attribute is determined by the type of TIMEX3. + For + instance, a DURATION must have a value that begins with the letter + ’P’ since durations + represent a period of time. This will be + elaborated on below in the value section. In addition, + some + optional attributes are used specifically with certain types of + temporal expressions. + uima.cas.String + + + value + The value attribute details which temporal information + is contained in the TIMEX3. + This value is given in an extended ISO + 8601 format. Examples: T24:00, 2001-01-12TEV, + 1984-01-03T12:00, + XXXX-12-02,1964-SU, P4M, PT20M + uima.cas.String + + + temporalFunction + Binary attribute which expresses that the value of the + temporal expression needs to + be determined via evaluation of a + temporal function. + uima.cas.Boolean + + + anchor + Optional attribute. It introduces the annotation of + the temporal expression to + which the TIMEX3 in question is + temporally anchored. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.temporal.UnambiguousTimex + Helper annotation type pointing to an most likely + unambiguous temporal expression. + The term '1992' could represent + a year, but also a measurement with that value. Other text spans like + '1.1.2015' are most likely + unambiguous dates, which can be represented + by this type. + de.averbis.extraction.types.CoreAnnotation + + + timex + The actual temporal expression. + de.averbis.textanalysis.types.temporal.Timex3 + + + + + de.averbis.textanalysis.types.temporal.WeekDay + Annotation indicating a weekday e.g., 'Monday'. + uima.tcas.Annotation + + + dayOfWeek + Number of the day, e.g., 1 for Monday + uima.cas.Integer + + + + + de.averbis.textanalysis.types.text.ArrowCloseBracket + Annotation representing a arrow close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.ArrowOpenBracket + Annotation representing a arrow open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.Asterisk + Annotation representing an asterisk. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Backslash + Annotation representing a backslash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Bracket + Annotation representing a bracket. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Bullet + Annotation representing a bullet. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.CWord + Annotation representing a capitalized word including complex words composed of + multiple tokens. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Caret + Annotation representing a caret. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.CloseBracket + Annotation representing a close bracket. + de.averbis.textanalysis.types.text.Bracket + + + de.averbis.textanalysis.types.text.CurlyCloseBracket + Annotation representing a curly close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.CurlyOpenBracket + Annotation representing a curly open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.Dash + Annotation representing a dash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.DollarSign + Annotation representing a dollar sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.DoubleQuote + Annotation representing a double quote. + de.averbis.textanalysis.types.text.Quote + + + de.averbis.textanalysis.types.text.Equal + Annotation representing a equals sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.EuroSign + Annotation representing a euro sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.FirstInDocument + First token or fragment in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FirstInLine + First token or fragment in a line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FirstLine + First line in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.FreeLine + First line of a paragraph that is preceded by an empty line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Hashtag + Annotation representing a hashtag. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.InBrackets + Annotation representing a text span in brackets (excluding arrow brackets). + de.averbis.textanalysis.types.text.TextSpan + + + de.averbis.textanalysis.types.text.InQuotes + Annotation representing a text span in quotes. + de.averbis.textanalysis.types.text.TextSpan + + + de.averbis.textanalysis.types.text.LastInDocument + Last token or fragment in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LastInLine + Last token or fragment in a line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LastLine + Last line in the document. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.LineFree + Last line of a paragraph that is followed by an empty line. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Minus + Annotation representing a minus sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Num1 + Annotation representing a number with one digit. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num1_2 + Annotation representing a number with one or two digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num2 + Annotation representing a number with two digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num2_4 + Annotation representing a number with two to four digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num3 + Annotation representing a number with three digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num4 + Annotation representing a number with four digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Num5 + Annotation representing a number with five digits. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.OpenBracket + Annotation representing a open bracket. + de.averbis.textanalysis.types.text.Bracket + + + de.averbis.textanalysis.types.text.Percent + Annotation representing a percent sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Plus + Annotation representing a plus sign. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.Quote + Annotation representing a quote. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.RoundCloseBracket + Annotation representing a round close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.RoundOpenBracket + Annotation representing a round open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.SingleQuote + Annotation representing a single quote. + de.averbis.textanalysis.types.text.Quote + + + de.averbis.textanalysis.types.text.Slash + Annotation representing a slash. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.SpecialChar + Annotation representing a special char. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.SquareCloseBracket + Annotation representing a square close bracket. + de.averbis.textanalysis.types.text.CloseBracket + + + de.averbis.textanalysis.types.text.SquareOpenBracket + Annotation representing a square open bracket. + de.averbis.textanalysis.types.text.OpenBracket + + + de.averbis.textanalysis.types.text.TextSpan + Annotation representing a text span. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Tilde + Annotation representing a tilde. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.TrimmedDocument + A trimmed version of the document annotation. + de.averbis.extraction.types.CoreAnnotation + + + de.averbis.textanalysis.types.text.Underscore + Annotation representing a underscore. + de.averbis.textanalysis.types.text.SpecialChar + + + de.averbis.textanalysis.types.text.VerticalBar + Annotation representing a vertical bar. + de.averbis.textanalysis.types.text.SpecialChar + + + org.apache.uima.ruta.type.ALL + + org.apache.uima.ruta.type.TokenSeed + + + org.apache.uima.ruta.type.AMP + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.ANY + + org.apache.uima.ruta.type.ALL + + + org.apache.uima.ruta.type.AnyLine + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.BREAK + + org.apache.uima.ruta.type.WS + + + org.apache.uima.ruta.type.CAP + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.COLON + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.COMMA + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.CW + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.DebugBlockApply + + org.apache.uima.ruta.type.DebugRuleApply + + + innerApply + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + + + + + org.apache.uima.ruta.type.DebugCreatedBy + + uima.cas.TOP + + + rule + + uima.cas.String + + + annotation + + uima.tcas.Annotation + + + script + + uima.cas.String + + + id + + uima.cas.Integer + + + + + org.apache.uima.ruta.type.DebugEvaluatedCondition + + uima.cas.TOP + + + element + + uima.cas.String + + + value + + uima.cas.Boolean + + + conditions + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + + + org.apache.uima.ruta.type.DebugFailedRuleMatch + + org.apache.uima.ruta.type.DebugRuleMatch + + + org.apache.uima.ruta.type.DebugInlinedBlock + + uima.cas.TOP + + + element + + uima.cas.String + + + asCondition + + uima.cas.Boolean + + + matched + + uima.cas.Boolean + + + inlinedRules + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + false + + + + + org.apache.uima.ruta.type.DebugMatchedRuleMatch + + org.apache.uima.ruta.type.DebugRuleMatch + + + org.apache.uima.ruta.type.DebugRuleApply + + org.apache.uima.ruta.type.DebugScriptApply + + + applied + + uima.cas.Integer + + + tried + + uima.cas.Integer + + + rules + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleMatch + + + id + + uima.cas.Integer + + + script + + uima.cas.String + + + + + org.apache.uima.ruta.type.DebugRuleElementMatch + + org.apache.uima.ruta.type.ProfiledAnnotation + + + baseCondition + + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + conditions + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugEvaluatedCondition + + + elements + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatches + false + + + inlinedConditionBlocks + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugInlinedBlock + false + + + + + org.apache.uima.ruta.type.DebugRuleElementMatches + + uima.cas.TOP + + + matches + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatch + + + element + + uima.cas.String + + + ruleAnchor + + uima.cas.Boolean + + + inlinedActionBlocks + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugInlinedBlock + false + + + + + org.apache.uima.ruta.type.DebugRuleMatch + + org.apache.uima.ruta.type.ProfiledAnnotation + + + elements + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugRuleElementMatches + + + matched + + uima.cas.Boolean + + + delegates + + uima.cas.FSArray + org.apache.uima.ruta.type.DebugScriptApply + + + + + org.apache.uima.ruta.type.DebugScriptApply + + org.apache.uima.ruta.type.ProfiledAnnotation + + + element + + uima.cas.String + + + timestamp + + uima.cas.Long + + + + + org.apache.uima.ruta.type.EXCLAMATION + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.EmptyLine + + org.apache.uima.ruta.type.AnyLine + + + org.apache.uima.ruta.type.EvalAnnotation + + uima.tcas.Annotation + + + original + The annotation that caused this outcome. + uima.tcas.Annotation + + + group + Identifier for the group of annotations and types in the evaluation. + uima.cas.String + + + + + org.apache.uima.ruta.type.FalseNegative + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.FalsePositive + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.Line + + org.apache.uima.ruta.type.AnyLine + + + org.apache.uima.ruta.type.MARKUP + + org.apache.uima.ruta.type.ALL + + + org.apache.uima.ruta.type.NBSP + + org.apache.uima.ruta.type.SPACE + + + org.apache.uima.ruta.type.NUM + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.PERIOD + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.PM + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.Paragraph + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.ProfiledAnnotation + + uima.tcas.Annotation + + + time + + uima.cas.Long + + + + + org.apache.uima.ruta.type.QUESTION + + org.apache.uima.ruta.type.SENTENCEEND + + + org.apache.uima.ruta.type.RutaAnnotation + + uima.tcas.Annotation + + + score + + uima.cas.Double + + + annotation + + uima.tcas.Annotation + + + + + org.apache.uima.ruta.type.RutaBasic + + uima.tcas.Annotation + + + replacement + + uima.cas.String + + + + + org.apache.uima.ruta.type.RutaColoring + + uima.tcas.Annotation + + + bgColor + + uima.cas.String + + + targetType + + uima.cas.String + + + fgColor + + uima.cas.String + + + selected + + uima.cas.Boolean + + + + + org.apache.uima.ruta.type.RutaFrame + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.RutaOptional + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.SEMICOLON + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.SENTENCEEND + + org.apache.uima.ruta.type.PM + + + org.apache.uima.ruta.type.SPACE + + org.apache.uima.ruta.type.WS + + + org.apache.uima.ruta.type.SPECIAL + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.SW + + org.apache.uima.ruta.type.W + + + org.apache.uima.ruta.type.Statistics + + uima.cas.TOP + + + name + + uima.cas.StringArray + + + total + + uima.cas.DoubleArray + + + amount + + uima.cas.IntegerArray + + + part + + uima.cas.DoubleArray + + + + + org.apache.uima.ruta.type.TokenSeed + + uima.tcas.Annotation + + + org.apache.uima.ruta.type.TruePositive + + org.apache.uima.ruta.type.EvalAnnotation + + + org.apache.uima.ruta.type.W + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.WS + + org.apache.uima.ruta.type.ANY + + + org.apache.uima.ruta.type.WSLine + + org.apache.uima.ruta.type.EmptyLine + + + org.apache.uima.ruta.type.html.A + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.B + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BIG + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BODY + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.BR + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.COMMENT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.DIV + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.EM + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.FONT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.FORM + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H1 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H2 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H3 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H4 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H5 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.H6 + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.HEAD + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.HTML + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.I + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.IMG + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.INPUT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.LI + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.LINK + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.META + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.OL + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.P + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.REMARK + + org.apache.uima.ruta.type.html.TAG + + + comment + + uima.cas.String + + + + + org.apache.uima.ruta.type.html.SCRIPT + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.SMALL + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.SPAN + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.STYLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TABLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TAG + + uima.tcas.Annotation + + + name + + uima.cas.String + + + expandedOffsets + + uima.cas.Boolean + + + attributeName + + uima.cas.StringArray + false + + + attributeValue + + uima.cas.StringArray + false + + + + + org.apache.uima.ruta.type.html.TBODY + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TD + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TH + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TITLE + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.TR + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.U + + org.apache.uima.ruta.type.html.TAG + + + org.apache.uima.ruta.type.html.UL + + org.apache.uima.ruta.type.html.TAG + + + + + + org.apache.uima.ruta.type.RutaFrame + uima.tcas.Annotation + org.apache.uima.ruta.type.RutaBasic + + + + + + true + true + false + + + diff --git a/src/test/resources/projects/it2/archetype.properties b/src/test/resources/projects/it2/archetype.properties deleted file mode 100644 index 095ecde..0000000 --- a/src/test/resources/projects/it2/archetype.properties +++ /dev/null @@ -1,5 +0,0 @@ -groupId=de.customer.nlp -artifactId=my-annotator -version=1 -package=de.customer.nlp -rutaScriptName=MyScript \ No newline at end of file diff --git a/src/test/resources/projects/it2/goal.txt b/src/test/resources/projects/it2/goal.txt deleted file mode 100644 index f7ffc47..0000000 --- a/src/test/resources/projects/it2/goal.txt +++ /dev/null @@ -1 +0,0 @@ -install \ No newline at end of file diff --git a/src/test/resources/projects/it2/reference/.buildpath b/src/test/resources/projects/it2/reference/.buildpath deleted file mode 100644 index bd83e30..0000000 --- a/src/test/resources/projects/it2/reference/.buildpath +++ /dev/null @@ -1,14 +0,0 @@ - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/test/resources/projects/it2/reference/input/.gitkeep b/src/test/resources/projects/it2/reference/input/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/src/test/resources/projects/it2/reference/output/.gitkeep b/src/test/resources/projects/it2/reference/output/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/src/test/resources/projects/it2/reference/pom.xml b/src/test/resources/projects/it2/reference/pom.xml deleted file mode 100644 index 95dabb5..0000000 --- a/src/test/resources/projects/it2/reference/pom.xml +++ /dev/null @@ -1,368 +0,0 @@ - - - - 4.0.0 - - de.customer.nlp - my-annotator - 1 - - jar - - - - 4.1.0 - - 3.1.0 - - 3.2.0 - 3.1.0 - 2.8.2 - 1.7.30 - - 1.8 - 1.8 - UTF-8 - - - - - org.slf4j - slf4j-api - ${slf4j-version} - provided - - - org.apache.uima - uimaj-core - ${uima-version} - provided - - - - org.apache.uima - ruta-core - ${ruta-version} - - - org.apache.uima - ruta-core-ext - ${ruta-version} - - - de.averbis.textanalysis - components-core-typesystem - ${core-typesystems-version} - - - de.averbis.textanalysis - measurement-typesystem - ${core-typesystems-version} - - - de.averbis.textanalysis - temporal-typesystem - ${core-typesystems-version} - - - de.averbis.textanalysis - numeric-value-typesystem - ${core-typesystems-version} - - - - de.averbis.textanalysis - clinical-section-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - components-health-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - diagnosis-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - ehr-information-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - laboratory-value-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - medical-disambiguation-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - medical-negation-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - medication-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - observation-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - oncology-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - pathology-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - patient-information-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - procedure-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - therapy-typesystem - ${health-typesystems-version} - - - de.averbis.textanalysis - tnm-typesystem - ${health-typesystems-version} - - - - junit - junit - 4.12 - test - - - org.apache.logging.log4j - log4j-core - ${log4j-version} - test - - - org.apache.logging.log4j - log4j-slf4j-impl - ${log4j-version} - test - - - - - - - src/main/ruta - - - src/main/resources - - - - - maven-failsafe-plugin - 2.21.0 - - - - integration-test - verify - - - - - - org.codehaus.mojo - exec-maven-plugin - 1.6.0 - - - generate-ruta-template - process-classes - - java - - - de.customer.nlp.GenerateConfiguredDescriptorTemplate - test - - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml - - - - - - - org.apache.uima - ruta-maven-plugin - ${ruta-version} - - - descriptors - process-classes - - generate - - - - ${basedir}/src/main/ruta - - **/*.ruta - - - ${project.build.directory}/generated-sources/ruta/descriptor/GeneratedBasicEngine.xml - ${project.build.directory}/generated-sources/ruta/descriptor - ${project.build.directory}/generated-sources/ruta/descriptor - RutaAnnotator - RutaTypeSystem - UTF-8 - true - false - -1 - - org.apache.uima.ruta - - true - - - - - - - - org.apache.maven.plugins - maven-resources-plugin - 3.1.0 - - - - copy-type-system - prepare-package - - copy-resources - - - UTF-8 - ${basedir}/target/classes - - - ${basedir}/target/generated-sources/ruta/descriptor - - **/*.xml - - - - - - - - copy-descriptors - prepare-package - - copy-resources - - - UTF-8 - ${basedir}/target/pearPackaging/desc - - - ${basedir}/target/generated-sources/ruta/descriptor/ - - **/*.xml - - - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - - - copy-dependencies - package - - copy-dependencies - - - ${basedir}/target/pearPackaging/lib - true - runtime - - - - - - org.apache.uima - PearPackagingMavenPlugin - ${uima-version} - true - - - - package - - desc/de/customer/nlp/MyScriptRutaAnnotator.xml - ${project.artifactId}-${project.version} - $main_root/resources - - - package - - - - - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.codehaus.mojo - exec-maven-plugin - [1.6.0,) - - java - - - - - - - - - - - - - - - diff --git a/src/test/resources/projects/it2/reference/src/main/java/de/customer/nlp/GenerateConfiguredDescriptorTemplate.java b/src/test/resources/projects/it2/reference/src/main/java/de/customer/nlp/GenerateConfiguredDescriptorTemplate.java deleted file mode 100644 index db38b2d..0000000 --- a/src/test/resources/projects/it2/reference/src/main/java/de/customer/nlp/GenerateConfiguredDescriptorTemplate.java +++ /dev/null @@ -1,76 +0,0 @@ -/* - * Copyright 2021 Averbis GmbH - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package de.customer.nlp; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStream; - -import org.apache.uima.analysis_engine.AnalysisEngineDescription; -import org.apache.uima.fit.factory.AnalysisEngineFactory; -import org.apache.uima.resource.ResourceInitializationException; -import org.apache.uima.resource.metadata.ConfigurationParameter; -import org.apache.uima.resource.metadata.ConfigurationParameterDeclarations; -import org.apache.uima.resource.metadata.ConfigurationParameterSettings; -import org.apache.uima.ruta.ReindexUpdateMode; -import org.apache.uima.ruta.engine.RutaEngine; -import org.xml.sax.SAXException; - -public class GenerateConfiguredDescriptorTemplate { - - public static void main(String[] args) throws ResourceInitializationException, - FileNotFoundException, SAXException, IOException { - - File outputFile = new File(args[0]); - outputFile.getParentFile().mkdirs(); - - AnalysisEngineDescription description = AnalysisEngineFactory - .createEngineDescription(RutaEngine.class); - - // activate complete reindexing mode for compatibility in OSGi environments - description.getAnalysisEngineMetaData().getConfigurationParameterSettings() - .setParameterValue(RutaEngine.PARAM_REINDEX_UPDATE_MODE, - ReindexUpdateMode.COMPLETE.name()); - - // optionally activate rule debug information by passing 'true' - configureIfAvailable(description, RutaEngine.PARAM_DEBUG, false); - configureIfAvailable(description, RutaEngine.PARAM_DEBUG_WITH_MATCHES, false); - - try (OutputStream os = new FileOutputStream(outputFile)) { - description.toXML(os); - } - } - - - private static void configureIfAvailable(AnalysisEngineDescription description, String param, - Object value) { - - ConfigurationParameterDeclarations configurationParameterDeclarations = description - .getAnalysisEngineMetaData().getConfigurationParameterDeclarations(); - ConfigurationParameterSettings configurationParameterSettings = description - .getAnalysisEngineMetaData().getConfigurationParameterSettings(); - - ConfigurationParameter configurationParameter = configurationParameterDeclarations - .getConfigurationParameter(null, param); - - if (configurationParameter != null) { - configurationParameterSettings.setParameterValue(param, value); - } - } - -} diff --git a/src/test/resources/projects/it2/reference/src/main/resources/META-INF/org.apache.uima.fit/types.txt b/src/test/resources/projects/it2/reference/src/main/resources/META-INF/org.apache.uima.fit/types.txt deleted file mode 100644 index 7343e46..0000000 --- a/src/test/resources/projects/it2/reference/src/main/resources/META-INF/org.apache.uima.fit/types.txt +++ /dev/null @@ -1 +0,0 @@ -classpath*:de/customer/nlp/**/*RutaTypeSystem.xml \ No newline at end of file diff --git a/src/test/resources/projects/it2/reference/src/main/ruta/de/customer/nlp/MyScript.ruta b/src/test/resources/projects/it2/reference/src/main/ruta/de/customer/nlp/MyScript.ruta deleted file mode 100644 index c6a7e1f..0000000 --- a/src/test/resources/projects/it2/reference/src/main/ruta/de/customer/nlp/MyScript.ruta +++ /dev/null @@ -1,6 +0,0 @@ -PACKAGE de.customer.nlp; - -TYPESYSTEM de.averbis.textanalysis.typesystems.AverbisTypeSystem; - -DECLARE SomeType; -Token{->SomeType}; \ No newline at end of file diff --git a/src/test/resources/projects/it2/reference/src/test/java/de/customer/nlp/PearPackageIT.java b/src/test/resources/projects/it2/reference/src/test/java/de/customer/nlp/PearPackageIT.java deleted file mode 100644 index a083114..0000000 --- a/src/test/resources/projects/it2/reference/src/test/java/de/customer/nlp/PearPackageIT.java +++ /dev/null @@ -1,76 +0,0 @@ -/* - * Copyright 2021 Averbis GmbH - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package de.customer.nlp; - -import java.io.File; -import java.util.Collection; - -import org.apache.commons.io.FileUtils; -import org.apache.uima.UIMAFramework; -import org.apache.uima.analysis_engine.AnalysisEngine; -import org.apache.uima.cas.CAS; -import org.apache.uima.fit.factory.JCasFactory; -import org.apache.uima.fit.util.SimpleNamedResourceManager; -import org.apache.uima.jcas.JCas; -import org.apache.uima.pear.tools.PackageBrowser; -import org.apache.uima.pear.tools.PackageInstaller; -import org.apache.uima.resource.PearSpecifier; -import org.apache.uima.ruta.engine.Ruta; -import org.apache.uima.util.XMLInputSource; -import org.junit.Assert; -import org.junit.Test; - -/* - * This integration test ensures that the annotator PEAR package fulfills - * the minimal requirements to be installed by the UIMA PackageInstaller - * and to process text - */ -public class PearPackageIT { - - @Test - public void testProcessText() throws Exception { - - PackageBrowser packageBrowser = this.installPackage(); - XMLInputSource xmlInputSource = new XMLInputSource(packageBrowser.getComponentPearDescPath()); - PearSpecifier pearSpecifier = UIMAFramework.getXMLParser().parsePearSpecifier(xmlInputSource); - AnalysisEngine analysisEngine = UIMAFramework.produceAnalysisEngine(pearSpecifier, new SimpleNamedResourceManager(), null); - - JCas jcas = JCasFactory.createJCas(); - CAS cas = jcas.getCas(); - jcas.setDocumentText("Test document text"); - - // mock some annotations - Ruta.apply(cas, "W{->Token};"); - - analysisEngine.process(jcas); - - Assert.assertEquals("SomeType annotations", 3, - cas.select("de.customer.nlp.MyScript.SomeType").count()); - } - - private PackageBrowser installPackage() { - - File installDir = new File("target/generated-test-sources"); - - Collection files = FileUtils.listFiles(new File("target/"), new String[] { "pear" }, - false); - - Assert.assertEquals(1, files.size()); - File pearPackage = files.iterator().next(); - - return PackageInstaller.installPackage(installDir, pearPackage, true, false); - } -} diff --git a/src/test/resources/projects/it2/reference/src/test/resources/log4j2.xml b/src/test/resources/projects/it2/reference/src/test/resources/log4j2.xml deleted file mode 100644 index b7c521f..0000000 --- a/src/test/resources/projects/it2/reference/src/test/resources/log4j2.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file