Return-Path: X-Original-To: apmail-ctakes-commits-archive@www.apache.org Delivered-To: apmail-ctakes-commits-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id C596010EE1 for ; Mon, 16 Dec 2013 16:33:55 +0000 (UTC) Received: (qmail 81525 invoked by uid 500); 16 Dec 2013 16:32:37 -0000 Delivered-To: apmail-ctakes-commits-archive@ctakes.apache.org Received: (qmail 81182 invoked by uid 500); 16 Dec 2013 16:32:18 -0000 Mailing-List: contact commits-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list commits@ctakes.apache.org Received: (qmail 80773 invoked by uid 99); 16 Dec 2013 16:31:33 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 16 Dec 2013 16:31:33 +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; Mon, 16 Dec 2013 16:31:20 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 6F94723889F7; Mon, 16 Dec 2013 16:30:57 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1551254 [4/26] - in /ctakes/branches/ytex: ctakes-ytex-res/ ctakes-ytex-res/.settings/ ctakes-ytex-res/src/ ctakes-ytex-res/src/main/ ctakes-ytex-res/src/main/resources/ ctakes-ytex-res/src/main/resources/org/ ctakes-ytex-res/src/main/reso... Date: Mon, 16 Dec 2013 16:30:40 -0000 To: commits@ctakes.apache.org From: vjapache@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20131216163057.6F94723889F7@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,34 @@ + + + org.apache.uima.java + true + org.apache.ctakes.ytex.uima.annotators.DateAnnotator + + DateAnnotator + + 1.0 + + + + + + + + + + + + + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,146 @@ + + + + org.apache.uima.java + true + org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator + + + DictionaryLookupAnnotator + + + + + + maxListSize + Specifies the maximum number of items to be returned + from an lucene query. + + Integer + false + false + + + + + maxListSize + + 2147483647 + + + + + + + + + + + + + org.apache.ctakes.typesystem.type.syntax.BaseToken + + org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation + + + + org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation + + + + + + + true + true + false + + + + + DbConnection + + org.apache.ctakes.core.resource.JdbcConnectionResource + + false + + + LookupDescriptor + + org.apache.ctakes.core.resource.FileResource + + false + + + + + + LookupDescriptorFile + + + file:org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml + + + org.apache.ctakes.core.resource.FileResourceImpl + + + + DbConnectionResrc + + + + + + + + DriverClassName + String + false + false + + + URL + String + false + false + + + Username + String + false + false + + + Password + String + false + false + + + + + org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl + + + + + + LookupDescriptor + LookupDescriptorFile + + + DbConnection + DbConnectionResrc + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,140 @@ + + + org.apache.uima.java + true + edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator + + + DictionaryLookupAnnotator + + + + + + maxListSize + Specifies the maximum number of items to be returned + from an lucene query. + Integer + false + false + + + + + maxListSize + + 2147483647 + + + + + + + + + + + + + + edu.mayo.bmi.uima.core.type.syntax.BaseToken + + + edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation + + edu.mayo.bmi.uima.core.type.textspan.Sentence + + + + edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention + + edu.mayo.bmi.uima.core.type.textsem.EntityMention + + + + + + + true + true + false + + + + + LookupDescriptor + + edu.mayo.bmi.uima.core.resource.FileResource + + false + + + DbConnection + + edu.mayo.bmi.uima.core.resource.JdbcConnectionResource + + false + + + + + + LookupDescriptorFile + + + ytex/uima/annotators/LookupDesc_SNOMED.xml + + edu.mayo.bmi.uima.core.resource.FileResourceImpl + + + + DbConnectionResrc + + + + + + + + DriverClassName + String + false + false + + + URL + String + false + false + + + Username + String + false + false + + + Password + String + false + false + + + + + ytex.uima.resource.InitableJdbcConnectionResourceImpl + + + + + + LookupDescriptor + LookupDescriptorFile + + + DbConnection + DbConnectionResrc + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,149 @@ + + + org.apache.uima.java + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DrugAggregatePlaintextProcessor + adaptation of cTAKES DrugAggregatePlaintextProcessor + + + + + ChunkCreatorClass + String + false + true + + Chunker/ChunkCreatorClass + + + + medicationRelatedSection + Section ids that need to be considered when generating + the DrugMentionAnnotation + String + true + false + + DrugMentionAnnotator/medicationRelatedSection + + + + + + ChunkCreatorClass + + edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator + + + + medicationRelatedSection + + + SIMPLE_SEGMENT + DEFAULT + CLINICAL_HISTORY + + + + + + + SegmentRegexAnnotator + SentenceDetectorAnnotator + TokenizerAnnotator + LvgAnnotator + ContextDependentTokenizerAnnotator + POSTagger + Chunker + DrugLookupWindowAnnotator + DictionaryLookupAnnotator + DrugMentionAnnotator + StatusAnnotator + NegationAnnotator + + + + Ordering + For subiterator + 1.0 + + edu.mayo.bmi.uima.core.type.textspan.Segment + edu.mayo.bmi.uima.core.type.textspan.Sentence + edu.mayo.bmi.uima.core.type.syntax.BaseToken + + + edu.mayo.bmi.uima.core.type.textspan.Sentence + edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation + + + + + + + + + + + + true + true + false + + + + + + LookupDesc_RXNORM + + + ytex/drugnerdesc/analysis_engine/LookupDesc_RXNORM.xml + + + + + + DictionaryLookupAnnotator/LookupDescriptor + LookupDesc_RXNORM + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,140 @@ + + + org.apache.uima.java + true + edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator + + + DictionaryLookupAnnotator + + + + + + maxListSize + Specifies the maximum number of items to be returned + from an lucene query. + Integer + false + false + + + + + maxListSize + + 2147483647 + + + + + + + + + + + + + + edu.mayo.bmi.uima.core.type.syntax.BaseToken + + + edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation + + edu.mayo.bmi.uima.core.type.textspan.Sentence + + + + edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention + + edu.mayo.bmi.uima.core.type.textsem.EntityMention + + + + + + + true + true + false + + + + + LookupDescriptor + + edu.mayo.bmi.uima.core.resource.FileResource + + false + + + DbConnection + + edu.mayo.bmi.uima.core.resource.JdbcConnectionResource + + false + + + + + + LookupDescriptorFile + + + ytex/drugnerdesc/analysis_engine/LookupDesc_RXNORM.xml + + edu.mayo.bmi.uima.core.resource.FileResourceImpl + + + + DbConnectionResrc + + + + + + + + DriverClassName + String + false + false + + + URL + String + false + false + + + Username + String + false + false + + + Password + String + false + false + + + + + ytex.uima.resource.InitableJdbcConnectionResourceImpl + + + + + + LookupDescriptor + LookupDescriptorFile + + + DbConnection + DbConnectionResrc + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,59 @@ + + + org.apache.uima.java + true + ytex.uima.annotators.MetaMapToCTakesAnnotator + + + MetaMapToCTakesAnnotator + + 1.0 + + + + checkMedications + Boolean + false + false + + + + + checkMedications + + false + + + + + + + + + + + + + + + org.metamap.uima.ts.Candidate + + + + edu.mayo.bmi.uima.core.type.textsem.EntityMention + edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation + + edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,34 @@ + + + org.apache.uima.java + true + ytex.uima.annotators.NamedEntityRegexAnnotator + + NamedEntityRegexAnnotator + + 1.0 + + + + + + + + + + + + + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,60 @@ + + + org.apache.uima.java + true + ytex.uima.annotators.NegexAnnotator + + NegexAnnotator + NegexAnnotator based on the original negex java code. + 1.0 + + + + negatePossibilities + Boolean + false + false + + + targetTypeName + String + false + false + + + + + negatePossibilities + + true + + + + targetTypeName + + ytex.uima.types.WordToken + + + + + + + + + + + + + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,35 @@ + + + org.apache.uima.java + true + org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator + + + SegmentAnnotator + + 1.0 + + + + + + + + + + + + + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,51 @@ + + + org.apache.uima.java + true + ytex.uima.annotators.SenseDisambiguatorAnnotator + + + SenseDisambiguatorAnnotator + + 1.0 + + + + metric + String + false + false + + + windowSize + Integer + false + false + + + + + + + + + + + + + + edu.mayo.bmi.uima.core.type.NamedEntity + + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,80 @@ + + + +org.apache.uima.java +true +org.apache.ctakes.ytex.uima.annotators.SentenceDetector + +Sentence Detector annotator +Discovers sentence boundaries. +2.1 +Mayo Clinic + + +SegmentsToSkip +String +true +false + + +SentenceModelFile +The file that contains the MaxEnt model used by the Sentence Dectector +String +false +true + + + + +SegmentsToSkip + + + + + +SentenceModelFile + +org/apache/ctakes/core/sentdetect/sd-med-model.zip + + + + + + + + + +org.apache.ctakes.typesystem.type.syntax.BaseToken + + +org.apache.ctakes.typesystem.type.textspan.Sentence + + + + + +true +true +false + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,148 @@ + + + org.apache.uima.java + false + + + + + + + + + + YTEXPipeline + ctakes AggregatePlaintextUMLSProcessor with following + changes: Replaced cTAKES NegationAnnotator with YTEX NegexAnnotator, + replaced cTAKES SimpleSegment with YTEX SegmentRegexAnnotator. + Reconfigured DictionaryLookup to use YTEX dictionary. + Added + DateAnnotator, SenseDisambiguatorAnnotator, + NamedEntityRegexAnnotator, DBConsumer + + + + + + analysisBatch + String + false + false + + DBConsumer/analysisBatch + + + + storeDocText + Boolean + false + false + + DBConsumer/storeDocText + + + + storeCAS + Boolean + false + false + + DBConsumer/storeCAS + + + + typesToIgnore + uima types (fully qualified class names) that should + not be saved in the database. + + String + true + false + + DBConsumer/typesToIgnore + + + + insertAnnotationContainmentLinks + should containment links be added + + Boolean + false + false + + DBConsumer/insertAnnotationContainmentLinks + + + + + + xmiOutputDirectory + + + + + + analysisBatch + + test + + + + storeDocText + + true + + + + storeCAS + + true + + + + insertAnnotationContainmentLinks + + true + + + + typesToIgnore + + + org.apache.ctakes.typesystem.type.syntax.ContractionToken + org.apache.ctakes.typesystem.type.syntax.NewlineToken + org.apache.ctakes.typesystem.type.syntax.PunctuationToken + + org.apache.ctakes.typesystem.type.syntax.SymbolToken + org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation + + org.apache.ctakes.typesystem.type.textsem.DateAnnotation + org.apache.ctakes.typesystem.type.textsem.FractionAnnotation + + org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation + + org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation + + org.apache.ctakes.typesystem.type.textsem.RangeAnnotation + + org.apache.ctakes.typesystem.type.textsem.TimeAnnotation + org.apache.ctakes.typesystem.type.syntax.NP + org.apache.ctakes.typesystem.type.syntax.VP + + + + + + + AggregatePlaintextUMLSProcessor + DBConsumer + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,343 @@ + + + org.apache.uima.java + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + YTEXPipeline + ctakes AggregatePlaintextUMLSProcessor with following + changes: Replaced cTAKES NegationAnnotator with YTEX NegexAnnotator, + replaced cTAKES SimpleSegment with YTEX SegmentRegexAnnotator. + Reconfigured DictionaryLookup to use YTEX dictionary. + Added + DateAnnotator, SenseDisambiguatorAnnotator, + NamedEntityRegexAnnotator, DBConsumer + + + + + + ChunkCreatorClass + String + false + true + + Chunker/ChunkCreatorClass + + + + xmiOutputDirectory + String + false + false + + DBConsumer/xmiOutputDirectory + + + + analysisBatch + String + false + false + + DBConsumer/analysisBatch + + + + storeDocText + Boolean + false + false + + DBConsumer/storeDocText + + + + storeCAS + Boolean + false + false + + DBConsumer/storeCAS + + + + typesToIgnore + uima types (fully qualified class names) that should + not be saved in the database. + + String + true + false + + DBConsumer/typesToIgnore + + + + insertAnnotationContainmentLinks + should containment links be added + + Boolean + false + false + + DBConsumer/insertAnnotationContainmentLinks + + + + + + ChunkCreatorClass + + edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator + + + + xmiOutputDirectory + + + + + + analysisBatch + + test + + + + storeDocText + + true + + + + storeCAS + + true + + + + insertAnnotationContainmentLinks + + true + + + + typesToIgnore + + + edu.mayo.bmi.uima.core.type.ContractionToken + edu.mayo.bmi.uima.core.type.syntax.NewlineToken + edu.mayo.bmi.uima.core.type.syntax.PunctuationToken + + edu.mayo.bmi.uima.core.type.syntax.SymbolToken + edu.mayo.bmi.uima.cdt.type.textsem.RomanNumeralAnnotation + + edu.mayo.bmi.uima.cdt.type.textsem.DateAnnotation + edu.mayo.bmi.uima.cdt.type.textsem.FractionAnnotation + + edu.mayo.bmi.uima.cdt.type.textsem.MeasurementAnnotation + + edu.mayo.bmi.uima.cdt.type.textsem.PersonTitleAnnotation + + edu.mayo.bmi.uima.cdt.type.textsem.RangeAnnotation + + edu.mayo.bmi.uima.cdt.type.textsem.TimeAnnotation + edu.mayo.bmi.uima.core.type.syntax.NP + edu.mayo.bmi.uima.core.type.syntax.VP + + + + + + + SegmentRegexAnnotator + SentenceDetectorAnnotator + TokenizerAnnotator + LvgAnnotator + ContextDependentTokenizerAnnotator + POSTagger + Chunker + AdjustNounPhraseToIncludeFollowingNP + AdjustNounPhraseToIncludeFollowingPPNP + LookupWindowAnnotator + DictionaryLookupAnnotator + NamedEntityRegexAnnotator + SenseDisambiguatorAnnotator + StatusAnnotator + NegationAnnotator + DateAnnotator + ExtractionPrepAnnotator + + + + Ordering + For subiterator + 1.0 + + edu.mayo.bmi.uima.core.type.textspan.Segment + edu.mayo.bmi.uima.core.type.textspan.Sentence + edu.mayo.bmi.uima.core.type.syntax.BaseToken + + + edu.mayo.bmi.uima.core.type.textspan.Sentence + edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation + + + + + + + + + + edu.mayo.bmi.uima.core.type.syntax.NewlineToken + + edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation + + edu.mayo.bmi.uima.core.type.syntax.WordToken + + edu.mayo.bmi.uima.core.type.syntax.VP + + edu.mayo.bmi.uima.core.type.refsem.UmlsConcept + + edu.mayo.bmi.uima.core.type.syntax.UCP + + edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation + + edu.mayo.bmi.uima.core.type.syntax.SymbolToken + + edu.mayo.bmi.uima.core.type.textspan.Sentence + + edu.mayo.bmi.uima.core.type.textspanSegment + + edu.mayo.bmi.uima.core.type.syntax.SBAR + + edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation + + edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation + + edu.mayo.bmi.uima.core.type.syntax.PunctuationToken + + edu.mayo.bmi.uima.core.type.Property + + edu.mayo.bmi.uima.core.type.Properties + + edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation + + edu.mayo.bmi.uima.core.type.syntax.PRT + + edu.mayo.bmi.uima.core.type.syntax.PP + + edu.mayo.bmi.uima.core.type.OntologyConcept + + edu.mayo.bmi.uima.core.type.syntax.NumToken + + edu.mayo.bmi.uima.core.type.syntax. + + edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation + + edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation + + edu.mayo.bmi.uima.core.type.syntax.Lemma + + edu.mayo.bmi.uima.core.type.syntax.LST + + edu.mayo.bmi.uima.core.type.syntax.INTJ + + edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation + + edu.mayo.bmi.uima.core.type.structured.DocumentID + + uima.tcas.DocumentAnnotation + edu.mayo.bmi.uima.core.type.textsem.DateAnnotation + + edu.mayo.bmi.uima.core.type.CopySrcAnnotation + + edu.mayo.bmi.uima.core.type.CopyDestAnnotation + + edu.mayo.bmi.uima.core.type.ContractionToken + + edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation + + edu.mayo.bmi.uima.core.type.syntax.Chunk + + edu.mayo.bmi.uima.core.type.syntax.CONJP + + edu.mayo.bmi.uima.core.type.syntax.BaseToken + + uima.cas.AnnotationBase + uima.tcas.Annotation + edu.mayo.bmi.uima.core.type.syntax.ADVP + + edu.mayo.bmi.uima.core.type.syntax.ADJP + + + + + + + true + true + false + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,92 @@ + + + org.apache.uima.java + org.apache.ctakes.ytex.uima.DBCollectionReader + + + DBcollectionReader + + 1.0 + + + + queryGetDocumentKeys + String + false + true + + + queryGetDocument + String + false + true + + + dbDriver + Fully qualified class name of jdbc driver to use to + retrieve documents. If null, will use db.driver from + ytex.properties + + String + false + false + + + dbURL + optional jdbc url to retrieve documents. If not + specified, will use default ytex jdbc url. Only use this if your + documents reside on a different database from the ytex database. If + needed, specify the username and password in the url. + + String + false + false + + + keyNameToLowerCase + convert key names to lower case, defaults to true + + Boolean + false + false + + + + + queryGetDocumentKeys + + select + + + + + queryGetDocument + + select doc_text from esld.dummy_document where site_id = + :site_id and uid = :uid and document_type_id = :document_type_id + + + + + + + + + + + + + + + + + + + + true + false + true + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,70 @@ + + + + + + + + + + InputDirectory + + examples/pubmed/abstracts + + + + + + + + + + + + + + + + + + + + + + + + + + typesToIgnore + + + edu.mayo.bmi.uima.core.type.ContractionToken + edu.mayo.bmi.uima.core.type.NewlineToken + edu.mayo.bmi.uima.core.type.PunctuationToken + edu.mayo.bmi.uima.core.type.SymbolToken + edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation + + edu.mayo.bmi.uima.cdt.type.DateAnnotation + edu.mayo.bmi.uima.cdt.type.FractionAnnotation + edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation + edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation + edu.mayo.bmi.uima.cdt.type.RangeAnnotation + edu.mayo.bmi.uima.cdt.type.TimeAnnotation + + edu.mayo.bmi.uima.chunker.type.VP + + + + + + + + + -1 + immediate + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,47 @@ + + + + + + + + + + InputDirectory + + examples/drugnertest + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + immediate + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,80 @@ + + + + + org.apache.uima.java + org.apache.uima.tools.components.FileSystemCollectionReader + + File System Collection Reader + Reads files from the filesystem. This CollectionReader may be used + with or without a CAS Initializer. If a CAS Initializer is supplied, it will + be passed an InputStream to the file and must populate the CAS from that + InputStream. If no CAS Initializer is supplied, this CollectionReader will + read the file itself and set treat the entire contents of the file as the + document to be inserted into the CAS. + 1.0 + The Apache Software Foundation + + + InputDirectory + Directory containing input files + String + false + true + + + Encoding + Character encoding for the documents. If not specified, + the default system encoding will be used. Note that this parameter + only applies if there is no CAS Initializer provided; otherwise, + it is the CAS Initializer's responsibility to deal with character + encoding issues. + String + false + false + + + Language + ISO language code for the documents + String + false + false + + + + + InputDirectory + + C:\java\apache-uima/examples/data + + + + + + + + + + + + + + + + + org.apache.uima.examples.SourceDocumentInformation + + + + + true + false + true + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,46 @@ + + + + + + + + + + InputDirectory + + examples/pubmed/abstracts + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + immediate + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,46 @@ + + + + + + + + + + InputDirectory + + examples/pubmed/abstracts + + + + + + + + + + + + + + + + + + + + + + + + + + + -1 + immediate + + + + Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml?rev=1551254&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml (added) +++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml Mon Dec 16 16:30:30 2013 @@ -0,0 +1,68 @@ + + + + + + + + + + InputDirectory + + examples/pubmed/abstracts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insertAnnotationContainmentLinks + + false + + + + + + + -1 + immediate + + + +