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From blee...@apache.org
Subject svn commit: r1410083 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext
Date Thu, 15 Nov 2012 22:46:27 GMT
Author: bleeker
Date: Thu Nov 15 22:46:26 2012
New Revision: 1410083

URL: http://svn.apache.org/viewvc?rev=1410083&view=rev
Log:
CMS commit to ctakes by bleeker

Added:
    incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext   (with props)

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext?rev=1410083&view=auto
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext (added)
+++ incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Core.mdtext Thu Nov 15 22:46:26
2012
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+Title:     cTAKES 2.6 Core
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you 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.
+
+# cTAKES 2.6 - Core
+
+## Overview of Core
+
+This project contains several annotators, including:
+
+  * a sentence detector annotator
+  * a tokenizer
+  * an annotator that does not update the CAS in any way
+  * an annotator that creates a single Segment annotation encompassing the entire document
text
+
+![](/images/icons/emoticons/information.png)
+
+End-of-line characters are considered end-of-sentence markers. Hyphenated
+words that appear in the hyphenated words list with frequency values greater
+than the FreqCutoff will be considered one token. Refer to [the tokenizer
+information on
+SourceForge.net](http://ohnlp.sourceforge.net/cTAKES/#tokenizer_annot).
+
+A sentence detector model is included with this project.
+
+![](/images/icons/emoticons/information.png)
+
+The model derives from a combination of GENIA, Penn Treebank (Wall Street
+Journal) and anonymized clinical data per Safe Harbor HIPAA guidelines. Prior
+to model building the clinical data was deidentified for patient names to
+preserve patient confidentiality. Any person name in the model will originate
+from non-patient data sources.
+
+## Analysis engines (annotators)
+
+### AggregateAE.xml
+
+This descriptor is included for testing. This descriptor is typically not used
+in a more complete pipeline. One or more of the individual analysis engines is
+normally included.
+
+### CopyAnnotator.xml
+
+This is a utility annotator that copies data from an existing JCas object into
+a new JCas object.
+
+### NullAnnotator.xml
+
+As its name implies, this annotator does nothing. It can be useful if you are
+using the UIMA CPE GUI and you are required to choose an analysis engine but
+you don't actually want to use one.
+
+### OverlapAnnotator.xml
+
+  * An annotator that modifies one annotation (begin and end offsets) or deletes one (or
both) of the annotations, when two annotations overlap. The action taken depends on the configuration
parameters. It can extend an annotation to encompass overlapping annotations. It can also
be configured to delete annotations of type A that are subsumed by other annotations of type
A if you only want the longest annotations of the given type to be kept.
+  * Refer to the _Javadoc_ for _edu.mayo.bmi.uima.core.ae.OverlapAnnotator_ for more details.
+
+### SentenceDetectorAnnotator.xml
+
+A wrapper around the [OpenNLP](http://opennlp.sourceforge.net/) sentence
+detector that creates Sentence annotations based on the location of end-of-
+line characters and on the output of the OpenNLP sentence detector. This
+annotator considers an end-of-line character as an end-of-sentence marker.
+Optionally it can skip certain sections of the document. See the section
+called [Running the sentence detector and
+tokenizer](http://ohnlp.sourceforge.net/cTAKES/#run_sentdetect_token_annot)
+for more details.
+
+**Parameters**  
+SegmentsToSkip
+
+(optional) the list of sections not to create Sentence annotations for.
+
+**Resources**  
+MaxentModelFile>
+
+the Maxent model sentence detector.
+
+### SimpleSegmentAnnotator.xml
+
+Creates a single Segment annotation, encompassing the entire document. For use
+prior to annotators that require a Segment annotation, when the pipeline does
+not contain a different annotator that creates Segment annotations. This
+annotator is used for plain text files, which doesn't have section (aka
+segment) tags; but not for CDA documents, as the CdaCasInitializer annotator
+creates Segment annotations.
+
+**Parameters**  
+SegmentID
+
+(optional) the identifier to use for the Segment annotation created.
+
+### TokenizerAnnotator.xml
+
+Tokenizes text according to Penn Treebank tokenization rules.  This is the
+default tokenizer for cTAKES as of cTAKES 2.0.
+
+**Parameters**  
+SegmentsToSkip
+
+(optional) the list of sections not to create token annotations for.
+
+### TokenizerAnnotatorVersion1.xml
+
+This is the original cTAKES tokenizer. Hyphenated words that appear in the
+hyphenated words list (HyphFreqFile) with frequency values greater than the
+FreqCutoff will be considered one token. See classes
+_edu.mayo.bmi.uima.core.ae.TokenizerAnnotator_ and
+_edu.mayo.bmi.nlp.tokenizer.Tokenizer_ for implementation details.
+
+**Parameters**  
+SegmentsToSkip
+
+(optional) the list of sections not to create token annotations for.
+
+FreqCutoff
+
+cutoff value for which entries to include from the hyphenated words
+list(HyphFreqFile)
+
+**Resources**  
+HyphFreqFile
+
+a file containing a list of hyphenated words and their frequency within some
+corpus.
+
+## Tools Training a sentence detector model
+
+To train a sentence detector that recognizes the same set of candidate end-of-
+sentence characters that the [SentenceDetectorAnnotator](http://ohnlp.sourcefo
+rge.net/cTAKES/#sentdetect_annot) uses:
+
+**java -cp <classpath> edu.mayo.bmi.uima.core.ae.SentenceDetector** **_<sents_file>_**
**_<model>_** **_<iters>_** **_<cut>_**  
+Where
+
+  * _<sents_file>_* is your sentences training data file, one sentence per
line, see an example in Example 4.1, "Sentence detector training data file sample".
+  * _<model>_* is the name of the model file to be created.
+  * _<iters>_* (optional) is the number of iterations for training.
+  * _<cut>_* (optional) is the cutoff value.
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+Eclipse users may run "SentenceDetector--train_ a_ new_model" launch.
+
+**Example 4.1. Sentence detector training data file sample**  
+One sentence per line.
+
+The boy ran.
+
+Did the girl run too?
+
+Yes, she did.
+
+Where did she go?
+
+### Verify you can train a sentence detector model successfully
+
+The sample model resources/sentdetect/sample_sd_included.mod was trained from
+data/test/sample_sd_training_sentences.txt, using default values (not
+specifying on the command line) for "iters" and "cut". You can verify your
+trained model with the sample one, using your favorite tool.
+
+### Using OpenNLP directly to train sentence detector model
+
+You can train a sentence detector directly using the OpenNLP sentence detector
+(SentenceDetectorME) with the default set of candidate end-of-sentence
+characters, using:
+
+The four parameters have the same meaning as the tool we provided, "infile"
+uses the same format as in Example 4.1, "Sentence detector training data file
+sample".
+
+## Running the sentence detector and tokenizer
+
+We provided a sentence detector CPE descriptor and a tokenizer CPE descriptor
+in this project. To run the CPE:
+
+**_<iters>_**java -cp <classpath> org.apache.uima.tools.cpm.CpmFrame
 
+Open
+
+**_<iters>_**desc/collection_processing_engine/SentenceDetecorCPE.xml to run
a sentence detector; or  
+**_<iters>_**desc/collection_processing_engine/SentencesAndTokensCPE.xml to
run a tokenizer
+
+The sentence detector CPE uses the analysis engines listed in
+desc/analysis_engine/SentenceDetectorAggregate.xml, and the tokenizer CPE uses
+those listed in desc/analysis_engine/SentencesAndTokensAggregate.xml. The two
+CPEs are defined to read from plain text file(s) in
+data/test/sample_notes_plaintext using the FilesInDirectoryCollectionReader.
+
+TIP Eclipse users may use the "SentenceDetector_annotator" and the "Tokenizer
+annotator" launches.
+
+## How do the CPEs work?
+
+Since the sentence annotator processes the text one section at a time, there
+must be at least one section (segment) annotation for the
+SentenceDetectorAnnotator to add Sentence annotations. Therefore the first
+analysis engine is the SimpleSegmentAnnotator, which creates a single Segment
+annotation that covers the entire text. Then the SentenceDetectorAnnotator
+analysis engine adds Sentence annotations. Then if you're running the
+tokenizer, the TokenizerAnnotator analysis engine adds annotations for tokens,
+such as PunctuationToken, WordToken, NewlineToken.
+
+Strictly speaking, it would not be necessary to run the
+SentenceDetectorAnnotator in order to test the TokenizerAnnotator. The
+TokenizerAnnotator does not require the presence of Sentence annotations.
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