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Posted to commits@ctakes.apache.org by ja...@apache.org on 2012/10/31 03:32:39 UTC
svn commit: r1403955 - in /incubator/ctakes/branches/SHARPn-cTAKES/files for
pipeline root: BUILDING CHANGES KEYS NOTICE README build.properties
build_step2.xml cTAKES_license.pdf
Author: james-masanz
Date: Wed Oct 31 02:32:38 2012
New Revision: 1403955
URL: http://svn.apache.org/viewvc?rev=1403955&view=rev
Log:
CTAKES-75 Housekeeping - Update README, LICENSE
Added:
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/CHANGES
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/KEYS
Removed:
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/cTAKES_license.pdf
Modified:
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/NOTICE
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/README
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build.properties
incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.xml
Modified: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/BUILDING?rev=1403955&r1=1403954&r2=1403955&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING Wed Oct 31 02:32:38 2012
@@ -1,8 +1,11 @@
-This information relates to building ctakes-2.6-incubating
+To build ctakes-2.6-incubating:
-First, check out all projects from SVN.
-For example, assertion and chunker are separate projects.
+NOTE: This documentation applies to ctakes-2.6-incubating but does not
+apply to ctakes-3.0-incubating or later.
+
+First, check out all projects from SVN
+For example, assertion and chunker are separate projects.
There are three ant scripts used to build cTAKES. The ant scripts
can be found in project 'files for pipeline root'.
@@ -32,4 +35,3 @@ Update those properties files for your e
Script build_step3 relies on the basedir value within build_script3.xml
Update the basedir value for your environment
-
\ No newline at end of file
Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/CHANGES
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/CHANGES?rev=1403955&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/CHANGES (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/CHANGES Wed Oct 31 02:32:38 2012
@@ -0,0 +1,13 @@
+
+ctakes-2.6-incubating
+=====================
+
+Added a relation extraction module (found in SVN as relation-extractor)
+with descriptors under cTAKESdesc/relationdesc.
+
+ctakes-2.6-incubating includes the following:
+ CTAKES-85 ElementRelation and AttributeRelation are missing arg1 and arg2
+ CTAKES-56 Type System updates for 2.6-incubating
+ CTAKES-33 Add Relation Extractor
+ CTAKES-15 Runtime exception for certain documents with Assertion module
+See https://issues.apache.org/jira/browse/CTAKES
Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/KEYS
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/KEYS?rev=1403955&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/KEYS (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/KEYS Wed Oct 31 02:32:38 2012
@@ -0,0 +1,161 @@
+This file contains the PGP keys of various developers.
+
+Users: pgp < KEYS
+ gpg --import KEYS
+Developers:
+ pgp -kxa <your name> and append it to this file.
+ (pgpk -ll <your name> && pgpk -xa <your name>)
+ >> this file.
+ (gpg --list-sigs <your name>
+ && gpg --armor --export <your name>) >>
+ this file.
+
+
+-----------------------------------------------------------------------------------
+
+pub 4096R/A720BC4E 2012-10-19
+uid Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+sig 3 A720BC4E 2012-10-19 Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+sub 4096R/1AF0B5B6 2012-10-19
+sig A720BC4E 2012-10-19 Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+
+pub 4096R/30F8F8E7 2012-10-26
+uid Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+sig 3 30F8F8E7 2012-10-26 Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+sub 4096R/41D15859 2012-10-26
+sig 30F8F8E7 2012-10-26 Pei Chen (CODE SIGNING KEY) <ch...@apache.org>
+
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+uid James Joseph Masanz <ja...@apache.org>
+sig 3 B6F78A30 2012-09-14 James Joseph Masanz <ja...@apache.org>
+sub 2048R/3E8CD1BD 2012-09-14
+sig B6F78A30 2012-09-14 James Joseph Masanz <ja...@apache.org>
+
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Modified: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/NOTICE?rev=1403955&r1=1403954&r2=1403955&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/NOTICE (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/NOTICE Wed Oct 31 02:32:38 2012
@@ -1,21 +1,46 @@
-
-Some material in the UMLS Metathesaurus is from copyrighted sources of
-the respective copyright holders. Users of the UMLS Metathesaurus are
-solely responsible for compliance with any copyright, patent or
-trademark restrictions and are referred to the copyright, patent or
-trademark notices appearing in the original sources, all of which are
-hereby incorporated by reference.
-
-This material includes SNOMED Clinical Terms® (SNOMED CT®) which is
-used by permission of the International Health Terminology Standards
-Development Organisation (IHTSDO). All rights reserved. SNOMED CT®,
-was originally created by The College of American Pathologists.
-"SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
-
-cTAKES includes the following vocabularies from the UMLS Metathesaurus:
- - SNOMED CT
- - NCI Thesaurus http://ncit.nci.nih.gov/
- - Medical Subject Headings http://www.nlm.nih.gov/mesh/
- - RxNorm http://www.nlm.nih.gov/research/umls/rxnorm/
-
-Please see the NOTICE file within each PEAR file for the other notices.
+Apache cTAKES
+Copyright 2012 The Apache Software Foundation
+
+This product includes software developed at
+The Apache Software Foundation (http://www.apache.org/).
+
+Portions of cTAKES were originally developed by
+Mayo Clinic and are licensed to the Apache Software
+Foundation under the "Software Grant License Agreement".
+Copyright (c) 2009 Mayo Foundation for Medical Education
+and Research (MFMER)
+
+Portions of cTAKES were originally developed by
+Boston Children's Hospital and are licensed to the Apache Software
+Foundation under the "Software Grant License Agreement".
+Copyright (c) 2012 Boston Children's Hospital.
+
+Portions of cTAKES were originally developed by
+University of Colorado and are licensed to the Apache Software
+Foundation under the "Software Grant License Agreement".
+Copyright (c) 2012 University of Colorado.
+
+Portions of cTAKES were originally developed by
+The MITRE corporation.
+Copyright (c) 2012 The MITRE Corporation.
+
+Some material in the UMLS Metathesaurus is from copyrighted sources of
+the respective copyright holders. Users of the UMLS Metathesaurus are
+solely responsible for compliance with any copyright, patent or
+trademark restrictions and are referred to the copyright, patent or
+trademark notices appearing in the original sources, all of which are
+hereby incorporated by reference.
+
+This material includes SNOMED Clinical Terms® (SNOMED CT®) which is
+used by permission of the International Health Terminology Standards
+Development Organisation (IHTSDO). All rights reserved. SNOMED CT®,
+was originally created by The College of American Pathologists.
+"SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
+
+cTAKES includes the following vocabularies from the UMLS Metathesaurus:
+ - SNOMED CT
+ - NCI Thesaurus http://ncit.nci.nih.gov/
+ - Medical Subject Headings http://www.nlm.nih.gov/mesh/
+ - RxNorm http://www.nlm.nih.gov/research/umls/rxnorm/
+
+Please see the NOTICE file within each PEAR file for the other notices.
Modified: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/README?rev=1403955&r1=1403954&r2=1403955&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/README (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/README Wed Oct 31 02:32:38 2012
@@ -1,5 +1,80 @@
-
-Javadocs are found within the docs directory.
-
-Other documentation is found online at
-https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/OHNLP_Documentation_and_Downloads
+
+Apache cTAKES (incubating)
+===============================
+
+Contents
+- Requirements
+- Introduction
+- Running the clinical documents pipeline
+ - AggregateCdaProcessor.xml for CDA documents conforming to the provided DTD.
+ - AggregatePlaintextProcessor.xml for plaintext documents.
+
+
+############
+Requirements
+############
+Java 1.6 is required to run cTAKES
+
+
+############
+Introduction
+############
+
+Detailed documentation can found at:
+http://incubator.apache.org/ctakes
+
+This project is the top-level, main project for processing a clinical document
+through the entire pipeline, including sentence detection, part of speech tagging,
+chunking, named entity recognition, context detection, and negation detection.
+
+
+############################################################################
+Running the clinical documents pipeline
+############################################################################
+
+The pipeline can process two types of documents
+ - plaintext files
+ - Clinical Document Architecture (CDA) XML files that conform to the DTD provided
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%
+AggregateCdaProcessor.xml for CDA documents conforming to the provided DTD.
+
+The file cTAKESdesc/analysis_engine/AggregateCdaProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the
+CdaCasInitialzer analysis engine, which reads CDA documents that conform
+to the DTD provided, and create Segment annotations based on the sections
+within the CDA document.
+
+Open this file using the Component Descriptor Editor as described in the tutorial.
+Click on the tab labeled "Aggregate" to observe that the Component Engine Flow (pipeline)
+defined by this descriptor includes CdaCasInitialzer as the first component.
+Observe that part of speech tagging (POSTagger) comes before chunking (Chunker), etc.
+
+Click on the tab labeled "Parameter Settings" to view the parameters set in this
+descriptor. The ChunkCreatorClass is set to edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator
+so that each phrase type gets its own type of annotation, rather than having all
+chunks be of type Chunk.
+
+The parameters are:
+- ChunkerCreatorClass - the full class name of an implementation of the
+ interface edu.mayo.bmi.uima.chunker.ChunkerCreator
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+AggregatePlaintextProcessor.xml for plaintext documents.
+
+The file cTAKESdesc/analysis_engine/AggregatePlaintextProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the
+SimpleSegmentAnnotator analysis engine, which creates a Segment annotation that
+wraps the entire plaintext document. Other annotators in the pipeline require
+at least 1 Segment annotation.
+
+Click on the tab labeled "Parameter Settings" to view the parameters set in this
+descriptor. The ChunkCreatorClass is set to edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator
+so that each phrase type gets its own type of annotation, rather than having all
+chunks be of type Chunk.
+
+The parameters are:
+- SegmentID - the identifier or name to assign to the Segment annotation
+- ChunkerCreatorClass - the full class name of an implementation of the
+ interface edu.mayo.bmi.uima.chunker.ChunkerCreator
Modified: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/build.properties?rev=1403955&r1=1403954&r2=1403955&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build.properties (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build.properties Wed Oct 31 02:32:38 2012
@@ -1,5 +1,5 @@
# Please do not comment or remove the following line.
-RELEASE_VERSION=2.5
+RELEASE_VERSION=2.6-incubating
# UIMA_HOME is the same as your environment variable
# when you installed Apache UIMA.
Modified: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/build_step2.xml?rev=1403955&r1=1403954&r2=1403955&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.xml (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.xml Wed Oct 31 02:32:38 2012
@@ -357,11 +357,6 @@
<filename name="KEYS" />
</fileset>
</copy>
- <copy todir="${CTAKES_HOME}">
- <fileset dir="${workspace.home}/files for pipeline root">
- <filename name="RELEASE_NOTES" />
- </fileset>
- </copy>
<copy todir="${CTAKES_HOME}">
<fileset dir="${workspace.home}/clinical documents pipeline">