Release Notes - cTAKES - Version 3.1.0 - HTML format

Sub-task

  • [CTAKES-108] - move ctakes-assertion dependencies into maven central repo
  • [CTAKES-203] - upgrade ctakes-assertion for cleartk-1.4.1
  • [CTAKES-204] - upgrade ctakes-relation-extractor for cleartk-1.4.1
  • [CTAKES-205] - upgrade ctakes-temporal for cleartk-1.4.1
  • [CTAKES-206] - upgrade managed version in main project pom and revert sub-project pom's to managed version

Bug

  • [CTAKES-14] - TimeMention is missing feature for what is being manually annotated as "class"
  • [CTAKES-53] - move UMLS out of Apache distribution
  • [CTAKES-97] - Remove unnecesssary OpenNLP tag dictionaries- it's built into the model since 1.5.x now- Thanks Joern
  • [CTAKES-100] - CAS does not contain any DocumentID
  • [CTAKES-101] - Term spotting pipelines returning 'unknown' classifications
  • [CTAKES-118] - Location of CPE Descriptor not changed in 3.1 update
  • [CTAKES-120] - Inconsistent or missing paths for AE and CPE directories
  • [CTAKES-130] - DictionaryLookupAnnotatorDB default config error
  • [CTAKES-139] - FileNotFoundException: .... SideEffectTypeSystem.xml (The system cannot find the path specified)
  • [CTAKES-141] - side effect descriptors referencing old package names - edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator
  • [CTAKES-142] - can't find lookup/snomed-like_codes_sample Side effect descriptors need relative path updates
  • [CTAKES-148] - java.io.FileNotFoundException: C:\cTAKES\xxxx\desc\Constituency Parser\desc\ConstituencyParserAnnotator.xml
  • [CTAKES-156] - java.io.FileNotFoundException: lookup/rxnorm_index when using DictionaryLookupAnnotator_sideEffectUMLS.xml
  • [CTAKES-157] - ctakes-side-effect .classpath has extraneous entry
  • [CTAKES-163] - testpatient_plaintext_1.txt not included in binary distribution
  • [CTAKES-166] - RelationExtractorAggregate.xml is missing a name
  • [CTAKES-177] - relation extractor should look for models on classpath
  • [CTAKES-190] - dictionary lookup should create specific XxxxMention annotations instead of more generic EntityMention
  • [CTAKES-194] - InvalidXMLException: An import could not be resolved. org.apache.ctakes.drugner.types.Typesystem DrugCNP2LookupWindow.xml
  • [CTAKES-201] - Bug in the path of umls validation url
  • [CTAKES-208] - LVG annotator: WordToken" used in java code but not declared in the XML type Descriptor.
  • [CTAKES-212] - [SECURITY] Frame injection vulnerability in published Javadoc
  • [CTAKES-214] - too few sentences
  • [CTAKES-216] - Medication Route in DrugNER - "IV" not identified as intravenous route
  • [CTAKES-218] - java.io.FileNotFoundException: at java.io.FileInputStream.open(Native Method)
  • [CTAKES-220] - some named entities not found, e.g."coronary artery disease" (chunker not labeling chunks correctly)
  • [CTAKES-221] - java.io.FileNotFoundException: org\apache\ctakes\dependency\parser\models\lemmatizer\dictionary-1.3.1.jar
  • [CTAKES-227] - Broca's -> PunctuationToken instead of ContractionToken - caused by apostrophe seen as sentence ending
  • [CTAKES-228] - SideEffect import type system
  • [CTAKES-229] - SvmVectorCreator reference within MipacqSvmVectorCreator.xml uses old package naming

New Feature

  • [CTAKES-69] - Add the code for reading Knowtator XML annotations into the UIMA type system.
  • [CTAKES-96] - Update Dependency Parser and Semantic Role Labeler - Thanks Jinho Choi and Lee Beecker
  • [CTAKES-129] - Populate the Drug NER named entity confidence attribute
  • [CTAKES-186] - Add ClearNLP POSTagger as optional AE to choose from
  • [CTAKES-187] - Add template filler component to fill CEM-based templates

Improvement

  • [CTAKES-12] - Upgrade to cTAKES components to latest Lucene version.
  • [CTAKES-18] - add XxxxEntity|EventMention types for other NEs similar to MedicationEventMention
  • [CTAKES-25] - retrain rest of models using OpenNLP 1.5
  • [CTAKES-32] - dictionary lookup creates new LookupTokens many times
  • [CTAKES-42] - user guide - Note that test1.xml uses CDA not plaintext AE
  • [CTAKES-57] - Type System updates for 3.x-incubating
  • [CTAKES-79] - Update TokenizerPTB unit test
  • [CTAKES-126] - On MS command prompt testing different versions with the CPE leads to errors as the first CTAKES_HOME sticks
  • [CTAKES-127] - Dependency Parser name includes full path in xmls
  • [CTAKES-140] - Allow clearTK to load read-only models from classpath instead of file URL.
  • [CTAKES-144] - The ctakes-distribution module should be excluded from deployment to maven central.
  • [CTAKES-160] - Exception Refinement
  • [CTAKES-161] - Take advantage of Java 1.5+ functionality
  • [CTAKES-164] - UMLS password could not be set in shell as ctakes.umlspw
  • [CTAKES-209] - Simplify how SentenceDetector models are loaded
  • [CTAKES-210] - Allow loading of Resources from InputStream instead of physical File
  • [CTAKES-211] - Remove special test models used for Unit Tests?

Task

  • [CTAKES-7] - Pre-Migration- Update/Migrate current cTAKES documentation
  • [CTAKES-181] - Post Graduation Tasks
  • [CTAKES-183] - Move the models from src/main/resources to their own projects {project}-res
  • [CTAKES-202] - upgrade to cleartk-1.4.1
  • [CTAKES-215] - Create a 3.1 release of Apache cTAKES
  • [CTAKES-260] - Doc version conflict: gettingstarted VS userguide

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