Return-Path: X-Original-To: apmail-incubator-ctakes-commits-archive@minotaur.apache.org Delivered-To: apmail-incubator-ctakes-commits-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 4728BC8AF for ; Fri, 15 Mar 2013 08:44:11 +0000 (UTC) Received: (qmail 53100 invoked by uid 500); 15 Mar 2013 08:44:11 -0000 Delivered-To: apmail-incubator-ctakes-commits-archive@incubator.apache.org Received: (qmail 52994 invoked by uid 500); 15 Mar 2013 08:44:09 -0000 Mailing-List: contact ctakes-commits-help@incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: ctakes-dev@incubator.apache.org Delivered-To: mailing list ctakes-commits@incubator.apache.org Received: (qmail 52971 invoked by uid 99); 15 Mar 2013 08:44:08 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 15 Mar 2013 08:44:08 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.4] (HELO eris.apache.org) (140.211.11.4) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 15 Mar 2013 08:43:58 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id D75FF23888E7; Fri, 15 Mar 2013 08:41:49 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1456800 [1/5] - in /incubator/ctakes/trunk/ctakes-relation-extractor: desc/analysis_engine/ resources/models/ src/main/java/org/apache/ctakes/relationextractor/ae/ src/main/java/org/apache/ctakes/relationextractor/ae/features/ src/main/jav... Date: Fri, 15 Mar 2013 08:41:49 -0000 To: ctakes-commits@incubator.apache.org From: stevenbethard@apache.org X-Mailer: svnmailer-1.0.8-patched Message-Id: <20130315084149.D75FF23888E7@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Author: stevenbethard Date: Fri Mar 15 08:41:48 2013 New Revision: 1456800 URL: http://svn.apache.org/r1456800 Log: CTAKES-177 - Looks for relation extractor models on classpath. Re-trains relation extractor models and re-generates descriptors to match. Should also fix CTAKES-166 and CTAKES-147. Added: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/frags_nolex_args.txt - copied unchanged from r1456797, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/frags_nolex_args.txt Removed: incubator/ctakes/trunk/ctakes-relation-extractor/resources/models/ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/MANIFEST.MF incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/encoders.ser incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/features-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/model.libsvm incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/outcome-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/training-data.libsvm incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/MANIFEST.MF incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/encoders.ser incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/features-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/frags_nolex_args.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/model.libsvm incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/outcome-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/training-data.libsvm incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/MANIFEST.MF incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/encoders.ser incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/features-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/model.libsvm incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/outcome-lookup.txt incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/training-data.libsvm Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/model.jar incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/em_pair/model.jar incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml?rev=1456800&r1=1456799&r2=1456800&view=diff ============================================================================== --- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml (original) +++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml Fri Mar 15 08:41:48 2013 @@ -1,42 +1,15 @@ - org.apache.uima.java true org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator - org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator + DegreeOfRelationExtractorAnnotator Descriptor automatically generated by uimaFIT unknown org.apache.ctakes.relationextractor.ae - GoldViewName - view containing the manual relation annotations; needed for training - String - false - false - - ProbabilityOfKeepingANegativeExample probability that a negative example should be retained for training Float @@ -44,20 +17,6 @@ false - PrintErrors - Print errors true/false - Boolean - false - false - - - ErrorOutputStream - If PARAM_PRINT_ERRORS is true, this indicates where to write files. If unspecified, it will output to STDOUT. - String - false - false - - org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName provides the full name of the ClassifierFactory class to be used. String @@ -87,12 +46,6 @@ - PrintErrors - - false - - - org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName org.cleartk.classifier.jar.JarClassifierFactory @@ -113,57 +66,13 @@ org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath - resources/models/degree_of/model.jar + /org/apache/ctakes/relationextractor/models/degree_of/model.jar - org.apache.ctakes.assertion.medfacts.types.Assertion - - uima.tcas.Annotation - - - assertionType - assertion type -- one of present, absent, possible, conditional, hypothetical, or assocated_with_someone_else - uima.cas.String - - - associatedConcept - - org.apache.ctakes.assertion.medfacts.types.Concept - - - - - org.apache.ctakes.assertion.medfacts.types.Concept - - uima.tcas.Annotation - - - conceptType - the concept type -- one of problem, treatment, or test - uima.cas.String - - - conceptText - - uima.cas.String - - - externalId - - uima.cas.Integer - - - originalEntityExternalId - - uima.cas.Integer - - - - org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree uima.tcas.Annotation @@ -378,6 +287,11 @@ uima.cas.Integer + + historyOf + + uima.cas.Integer + @@ -672,7 +586,7 @@ org.apache.ctakes.typesystem.type.refsem.OntologyConcept Ontologies (e.g., SNOMED-CT) provide an expert semantic representation for concepts. They typically assign a code to a concept and normalize across various textual representations of that concept. IdentifiedAnnotation and Elements may point to these normalized concept representations to indicate clinical concepts. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.OntologyConcept +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.OntologyConcept uima.cas.TOP @@ -866,7 +780,7 @@ More qualifying information on how the p org.apache.ctakes.typesystem.type.refsem.UmlsConcept Concepts in the Unified Medical Language System (UMLS) Metathesaurus have a concept unique identifier (CUI) and a type unique identifier (TUI, i.e., semantic type) which are curated, normalized codes. For example, "pain" would have a cui=C0030193 and tui=T184. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.UmlsConcept +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.UmlsConcept org.apache.ctakes.typesystem.type.refsem.OntologyConcept @@ -887,9 +801,31 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.relation.ElementRelation + org.apache.ctakes.typesystem.type.relation.AffectsTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + + org.apache.ctakes.typesystem.type.relation.AspectualTextRelation + A UMLS relation between clinical elements. + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.AttributeRelation A real-world relationship between an Element and an Attribute. org.apache.ctakes.typesystem.type.relation.Relation + + + arg1 + + org.apache.ctakes.typesystem.type.refsem.Element + + + arg2 + + org.apache.ctakes.typesystem.type.refsem.Attribute + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation @@ -922,6 +858,11 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.CoreferenceRelation A coreference pair, with antecedent as arg1 and anaphor as arg2 org.apache.ctakes.typesystem.type.relation.BinaryTextRelation @@ -932,9 +873,26 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.relation.AttributeRelation + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.ElementRelation A super-type referring to real-world semantic relationships, e.g., TemporalRelations between two Events. org.apache.ctakes.typesystem.type.relation.Relation + + + arg1 + + org.apache.ctakes.typesystem.type.refsem.Element + + + arg2 + + org.apache.ctakes.typesystem.type.refsem.Element + + org.apache.ctakes.typesystem.type.relation.LocationOf @@ -942,11 +900,26 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.relation.ElementRelation + org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + + org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.ManifestationOf A UMLS relation between clinical elements. org.apache.ctakes.typesystem.type.relation.ElementRelation + org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.Relation A superclass for semantic relationships between Elements. For example, one might consider TemporalRelations or UMLSRelations between a Medication and a Disorder. The "category" feature indicates what kind of relation it is. uima.cas.TOP @@ -1017,11 +990,21 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.relation.ElementRelation + org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation + + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.TemporalRelation Based on ISO TimeML's TLINK. org.apache.ctakes.typesystem.type.relation.ElementRelation + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + A UMLS relation between clinical elements. + org.apache.ctakes.typesystem.type.relation.BinaryTextRelation + + org.apache.ctakes.typesystem.type.relation.UMLSRelation A biomedical relationship between two spans of text that have been mapped to UMLS concepts. Inherits "category" from Relation, with values such as affects, causes, complicates, contraindicates, degree_of, etc. org.apache.ctakes.typesystem.type.relation.BinaryTextRelation @@ -1074,6 +1057,18 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.structured.DocumentClassification + + uima.cas.TOP + + + label + + uima.cas.String + + + + org.apache.ctakes.typesystem.type.structured.DocumentID Equivalent to cTAKES: org.apache.ctakes.typesystem.type.DocumentID, but its supertype changed to uima.cas.TOP uima.cas.TOP @@ -1189,7 +1184,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.BaseToken A supertype for tokens subsuming word, punctuation, symbol, newline, contraction, or number. Includes parts of speech, which are grammatical categories, e.g., noun (NN) or preposition (IN) that use Penn Treebank tags with a few additions. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.BaseToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.BaseToken uima.tcas.Annotation @@ -1294,7 +1289,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.ContractionToken Differentiates a token as being a contraction rather than a punctuation, symbol, newline, word, or number. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.ContractionToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.ContractionToken org.apache.ctakes.typesystem.type.syntax.BaseToken @@ -1312,7 +1307,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.Lemma Stores a lemma (canonical form of a token). Inherits from uima.cas.TOP, allowing for reuse of standardized forms across the CAS. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.Lemma +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Lemma uima.cas.TOP @@ -1336,13 +1331,13 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.NewlineToken Differentiates a token as being a newline rather than a punctuation, symbol, contraction, word, or number. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.NewlineToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.NewlineToken org.apache.ctakes.typesystem.type.syntax.BaseToken org.apache.ctakes.typesystem.type.syntax.NumToken Differentiates a token as being a number rather than a punctuation, symbol, newline, word, or contraction. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.NumToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.NumToken org.apache.ctakes.typesystem.type.syntax.BaseToken @@ -1372,7 +1367,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.PunctuationToken Differentiates a token as being punctuation rather than a contraction, symbol, newline, word, or number. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.PunctuationToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.PunctuationToken org.apache.ctakes.typesystem.type.syntax.BaseToken @@ -1389,7 +1384,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.SymbolToken Differentiates a token as being a symbol rather than a punctuation, contraction, newline, word, or number. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.SymbolToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.SymbolToken org.apache.ctakes.typesystem.type.syntax.BaseToken @@ -1485,7 +1480,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.syntax.WordToken Differentiates a token as being a word rather than a punctuation, symbol, newline, contraction, or number. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.WordToken +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.WordToken org.apache.ctakes.typesystem.type.syntax.BaseToken @@ -1511,6 +1506,77 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation + A cue phrase indicating potential negation, uncertainty, or conditional + uima.tcas.Annotation + + + id + + uima.cas.Integer + + + cuePhraseCategory + + uima.cas.String + + + cuePhraseAssertionFamily + which assertion family this cue phrase belongs to (negation, uncertainty, or conditional) + uima.cas.String + + + cuePhraseFirstWord + first word of cue phrase + uima.cas.String + + + cuePhrase + cue phrase itself (from lookup list) + uima.cas.String + + + + + org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention + A text string that refers to a (AnatomicalSite) Entity. A body part or area, corresponding to the UMLS semantic group of Anatomy. Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EntityMention + + + bodyLaterality + + org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier + + + bodySide + + org.apache.ctakes.typesystem.type.textsem.BodySideModifier + + + + + org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier + The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.). This is finer-grained to allow combinations of values. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.BodySideModifier + Value set: unmarked (default), left, right, bilateral + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.ConditionalModifier + The Conditional modifier refers to mentions which could exist under certain circumstances. If indicated, there are conditions under which an associated Named Entity mention might not be truly asserted. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + org.apache.ctakes.typesystem.type.textsem.ContextAnnotation Contextual information of an entity. Equivalent to cTAKES: edu.mayo.bmi.uima.context.type.ContextAnnotation org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation @@ -1528,11 +1594,83 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.textsem.CourseModifier + An indication of progress or decline of a condition. Value set: unmarked (default), changed, increased, decreased, improved, worsened, resolved + org.apache.ctakes.typesystem.type.textsem.Modifier + + org.apache.ctakes.typesystem.type.textsem.DateAnnotation Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.DateAnnotation org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention + A text string that refers to a (DiseaseDisorder) Event. This is from the UMLS semantic group of Disorders (except that Sign and Symptom types are separate). Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EventMention + + + alleviatingFactor + + org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation + + + associatedSignSymptom + + org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation + + + bodyLaterality + + org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier + + + bodySide + + org.apache.ctakes.typesystem.type.textsem.BodySideModifier + + + bodyLocation + + org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation + + + course + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + duration + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + endTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + exacerbatingFactor + + org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation + + + startTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + relativeTemporalContext + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + severity + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + + org.apache.ctakes.typesystem.type.textsem.EntityMention A text string (IdentifiedAnnotation) that refers to an Entity. org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation @@ -1562,6 +1700,30 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + org.apache.ctakes.typesystem.type.textsem.GenericModifier + The Generic modifier indicates that a named entity mention is generic, i.e., not related to the instance of a disorder, sign/symptom, etc. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + + org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier + An indication of explicit mentioning of a past history. The indicator captures only very explicit mentions of historicity. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation Any span of text that has been discovered or flagged for some reason, such as a Named Entity. Allows for mapping to an ontology. Generalized from cTAKES: org.apache.ctakes.typesystem.type.IdentifiedAnnotation. uima.tcas.Annotation @@ -1627,17 +1789,115 @@ Equivalent to cTAKES: org.apache.ctakes. uima.cas.String + + historyOf + + uima.cas.Integer + - org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation - Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation - org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier + An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result. + org.apache.ctakes.typesystem.type.textsem.Modifier - org.apache.ctakes.typesystem.type.textsem.MedicationEventMention - A text string (EventMention and therefore IdentifiedAnnotation) that refers to a (Medication) Event. - org.apache.ctakes.typesystem.type.textsem.EventMention + org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier + Signals that the lab value was estimated, e.g., "GFR (estimated): 81". True means that there is an indicator signalling that there was an estimation of the value. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + + org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier + Test result interpretations organized in a valued list e.g., "rare cells seen" or "few cells seen" in urinalysis, now combined with very_abnormal and abnormal. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + value + + uima.cas.String + + + + + org.apache.ctakes.typesystem.type.textsem.LabMention + A text string that refers to a (Lab) Event. This is from the UMLS semantic group of Laboratory Procedures. Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EventMention + + + abnormalInterpretation + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + deltaFlag + + org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier + + + labValue + + org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation + + + ordinalInterpretation + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + referenceRangeNarrative + + org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier + + + + + org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier + Holds a narrative (i.e. string) reference range + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.LabValueModifier + Quantitative results of a laboratory, with number and unit. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation + Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation + org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + + + org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier + Indication of whether the medication is mentioned in the context of Allergies. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + + org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier + Dosage indicates how much of a prescribed drug should be taken. E.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks" + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier + The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks" + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationEventMention + A text string (EventMention and therefore IdentifiedAnnotation) that refers to a (Medication) Event. + org.apache.ctakes.typesystem.type.textsem.EventMention medicationFrequency @@ -1687,6 +1947,93 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier + Form of this medication. Value set includes tablet, capsule, liquid, inhalant, gel, other, etc. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier + How often a medication should be used. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationMention + A text string that refers to a (Medication) Event. This is an Event from the UMLS semantic group of Chemicals and Drugs, pruned by RxNORM source. Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EventMention + + + medicationAllergy + + org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier + + + medicationFrequency + + org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier + + + medicationDuration + + org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier + + + medicationRoute + + org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier + + + medicationStatusChange + + org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier + + + medicationDosage + + org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier + + + medicationStrength + + org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier + + + medicationForm + + org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier + + + startDate + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + endDate + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + relativeTemporalContext + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + + + org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier + Means by which the medication was taken or administered. Value set includes Topical, Enteral_Oral, Parenteral_Intravenous, Other, undetermined, etc. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier + Status refers to the whether the medication is currently being taken or not. Value set: start, stop, increase, decrease, no change. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier + Strength indicates the strength number and unit of the prescribed drug. E.g. "5 mg" in "one 5 mg tablet twice-a-day for 2 weeks" + org.apache.ctakes.typesystem.type.textsem.Modifier + + org.apache.ctakes.typesystem.type.textsem.Modifier A text string (IdentifiedAnnotation) that refers to an Attribute. org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation @@ -1696,6 +2043,11 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.refsem.Attribute + + category + + uima.cas.String + @@ -1704,6 +2056,18 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + org.apache.ctakes.typesystem.type.textsem.PolarityModifier + Used to indicate that a procedure or assertion did not occur or does not exist. If indicated, negation is present and polarity should be -1. If not indicated, negation is not present and polarity should be +1 by default. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + + + + org.apache.ctakes.typesystem.type.textsem.Predicate Predicates are typically verbs and may participate in SemanticRoleRelations. Follows PropBank standards with a few clinical additions. uima.tcas.Annotation @@ -1722,6 +2086,70 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier + Corresponds to the UMLS Devices semantic group: medical device and research device. +Example: arterial line has a Medical Device semantic type. This is qualifying information on how a procedure was done. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.ProcedureMention + A text string that refers to a (Procedure) Event. This is from the UMLS semantic group of Procedures (except that Laboratory procedures are separate). Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EventMention + + + bodyLaterality + + org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier + + + bodySide + + org.apache.ctakes.typesystem.type.textsem.BodySideModifier + + + bodyLocation + + org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation + + + procedureDevice + + org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier + + + duration + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + endTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + method + + org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier + + + startTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + relativeTemporalContext + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + + + org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier + The way or the equipment used to give or administration something (medication, test). This corresponds to the Procedures UMLS semantic group. +More qualifying information on how the procedure was done. + org.apache.ctakes.typesystem.type.textsem.Modifier + + org.apache.ctakes.typesystem.type.textsem.RangeAnnotation Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RangeAnnotation org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation @@ -1766,6 +2194,85 @@ Equivalent to cTAKES: org.apache.ctakes. + org.apache.ctakes.typesystem.type.textsem.SeverityModifier + An explicitly-mentioned indication of the seriousness of a condition. Value Set: unmarked (default), severe, moderate, slight + org.apache.ctakes.typesystem.type.textsem.Modifier + + + org.apache.ctakes.typesystem.type.textsem.SignSymptomMention + A text string that refers to a (SignSymptom) Event. This is from the UMLS semantic group of Sign or Symtom. Based on generic Clinical Element Models (CEMs) + org.apache.ctakes.typesystem.type.textsem.EventMention + + + alleviatingFactor + + org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation + + + bodyLaterality + + org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier + + + bodySide + + org.apache.ctakes.typesystem.type.textsem.BodySideModifier + + + bodyLocation + + org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation + + + course + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + duration + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + endTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + exacerbatingFactor + + org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation + + + severity + + org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation + + + startTime + + org.apache.ctakes.typesystem.type.textsem.TimeMention + + + relativeTemporalContext + + org.apache.ctakes.typesystem.type.relation.TemporalTextRelation + + + + + org.apache.ctakes.typesystem.type.textsem.SubjectModifier + The person the observation is on, i.e., a Person mention. This modifier refers to the entity experiencing the disorder. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + value + + uima.cas.String + + + + org.apache.ctakes.typesystem.type.textsem.TimeAnnotation Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.TimeAnnotation org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation @@ -1776,10 +2283,32 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + date + + org.apache.ctakes.typesystem.type.refsem.Date + + time org.apache.ctakes.typesystem.type.refsem.Time + + timeClass + DATE, DURATION, QUANTIFIER, PREPOSTEXP, etc. + uima.cas.String + + + + + org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier + An introduction of a measure of doubt into a statement. If indicated, there is uncertainty. + org.apache.ctakes.typesystem.type.textsem.Modifier + + + indicated + + uima.cas.Boolean + @@ -1814,7 +2343,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima. org.apache.ctakes.typesystem.type.textspan.Segment A section of a clinical text, e.g., Diagnosis, Current Medications, Problem List. Different segments often have differing sublanguages and clinical relevance. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.Segment +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Segment uima.tcas.Annotation @@ -1827,7 +2356,7 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.textspan.Sentence Sentences may or may not be fully-formed and grammatical. They form the unit of analysis for some downstream components (e.g., constituency parsers). -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.Sentence +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Sentence uima.tcas.Annotation @@ -1845,7 +2374,7 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.util.Pair An Attribute-Value tuple. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.Property +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Property uima.cas.TOP @@ -1863,7 +2392,7 @@ Equivalent to cTAKES: org.apache.ctakes. org.apache.ctakes.typesystem.type.util.Pairs A brute force "hash" that stores multiple Pairs in a list. -Equivalent to cTAKES: org.apache.ctakes.typesystem.type.Properties +Equivalent to cTAKES: edu.mayo.bmi.uima.core.type.Properties uima.cas.TOP