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From blee...@apache.org
Subject svn commit: r1410087 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Dictionary-Lookup.mdtext
Date Thu, 15 Nov 2012 22:52:03 GMT
Author: bleeker
Date: Thu Nov 15 22:52:03 2012
New Revision: 1410087

URL: http://svn.apache.org/viewvc?rev=1410087&view=rev
Log:
CMS commit to ctakes by bleeker

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

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Dictionary-Lookup.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Dictionary-Lookup.mdtext?rev=1410087&view=auto
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Dictionary-Lookup.mdtext (added)
+++ incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Dictionary-Lookup.mdtext Thu
Nov 15 22:52:03 2012
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+Title:     cTAKES 2.6 Dictionary Lookup
+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 - Dictionary Lookup
+
+## Overview of Dictionary Lookup
+
+The dictionary lookup annotator finds the entries from one or more
+dictionaries that match the document text in some way. Within this annotator,
+these matches are called lookup hits.
+
+The dictionary lookup annotator is very customizable. It can look for matches
+where the words in the dictionary entries appear in the same order as the
+words in the document text, or it can look for permutations of the words from
+the dictionary. Moreover, it can look just for exact matches of the words, or
+it can also look for matches to the canonical forms of the words.
+
+Searches for a lookup hit are limited to within windows, where the window type
+is defined in the LookupDescriptorFile. A window can be the words that fall
+within the same Sentence, the same Chunk, the same LookupWindowAnnotation or
+any other annotation. See the clinical documents pipeline project for an
+example of an analysis engine (LookupWindowAnnotator.xml) that creates
+LookupWindowAnnotations.
+
+## Implementation of Dictionry Lookup
+
+Starting with version 1.3, cTAKES includes UMLS (SNOMED CT and RxNorm)
+dictionaries. To use those dictionaries, you must have a UMLS username and
+password, and an internet connection (to verify your UMLS username and
+password). If you do not have a UMLS username and/or are not interested in
+those dictionaries, you can build your own or use the small sample
+dictionaries (see below).
+
+The behavior of the dictionary lookup annotator is controlled by the
+parameters and resources defined in the analysis engine descriptor, and by the
+contents of the resource called the LookupDescriptorFile.
+
+For example, if the analysis engine descriptor DictionaryLookup.xml contains a
+resource named LookupDescriptorFile with value lookup/LookupDesc.xml, then the
+parameter settings and resources named within DictionaryLookup.xml, together
+with the values within lookup/LookupDesc.xml will control the actions of the
+dictionary lookup annotator.
+
+The lookupInitializer and lookupConsumer classes are specified within the
+LookupDescriptorFile. The algorithm used for looking up the terms is defined
+by the lookupInitializer, which creates the lookup hits. The lookupConsumer
+adds annotations to the CAS for some or all of the lookup hits.
+
+An example of adding only some of the lookup hits to the CAS is if you have a
+dictionary of RxNorm terms with their RxNorm codes, and a dictionary of terms
+from the OrangeBook, and want to create annotations for those terms that are
+in the OrangeBook that also have an RxNorm code.
+
+This can be done using class
+edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl as the
+lookupInitializer, and using class OrangeBookFilterConsumerImpl as the
+lookupConsumer, provided you have the RxNorm dictionary, and you configure the
+LookupDescriptorFile resource to use your RxNorm dictionary.
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+Dictionary entries need to have been tokenized the way the pipeline tokenizes
+the document text. For example, the lookup algorithm will not find a lookup
+hit if a dictionary entry is "ear, skin" but the document text contains the
+same text ("ear, skin") and the pipeline has tokenized that text as the three
+tokens "ear" "," "skin". To find a lookup hit for the three tokens, the
+dictionary entry should be tokenized, with a space before the comma: "ear ,
+skin".
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+Editing dictionary lookup AE descriptors in Eclipse
+
+The analysis engine descriptors for this annotator use elements of type
+configurableDataResourceSpecifier. These cannot be modified from the
+Parameters or Resources tabs of the Component Descriptor Editor (at least not
+in UIMA 2.2). To view these values or edit them, use the Sources tab or open
+the descriptor with a text editor.
+
+To determine the LookupDescriptorFile for an analysis engine, open the
+analysis engine descriptor (e.g. DictionaryLookupannotator.xml) and note the
+URL for the LookupDescriptorFile resource (e.g. lookup/LookupDesc.xml).
+
+A LookupDescriptorFile such as lookup/LookupDesc.xml, found in resources/,
+defines the dictionary(s) used, and the classes that interact with the
+dictionary(s). The implementation tag identifies the type of dictionary:
+Lucene index (luceneImpl), database (jdbcImpl), or delimited flat file
+(csvImpl). See class edu.mayo.bmi.uima.lookup.ae.LookupParseUtilities.java for
+implementation details.
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+To better understand the dictionary lookup annotator code you could start by
+reading the Javadoc API for the classes DictionaryLookupAnnotator.java and
+FirstTokenPermutationImpl.java.'
+
+### DictionaryLookupAnnotatorUMLS.xml
+
+This uses the bundled UMLS (SNOMED CT and RxNorm) dictionaries. Before using
+this analysis engine descriptor, update the UMLSUser and UMLSPW parameters
+within this descriptor with your UMLS username and password. You will need to
+have an active connection to the internet so your UMLS username and password
+can be verified.
+
+### DictionaryLookupAnnotator.xml
+
+This uses the small sample dictionaries. This annotator can be run out-of-the-
+box without modifying any parameters, but annotates a very limited set of
+terms such as carcinoma, aspirin, knee, and pain.
+
+### DictionaryLookupannotatorCSV.xml
+
+This is an example of how to use a dictionary contained in a delimited file
+rather than a database or a Lucene index. This is only recommended for small
+dictionaries.
+
+### DictionaryLookupannotatorDB.xml
+
+This is a skeleton of how you could use a dictionary contained in a database
+that can be accessed via a JDBC driver instead of using a Lucene index or flat
+file.
+
+Refer also to the page on [dictionaries in the cTAKES documentation on SourceF
+orge](http://ohnlp.sourceforge.net/cTAKES/#boost_performance%7Cinstalling).
+
+## Sample dictionaries
+
+This project includes two sample dictionaries that are used by default:
+
+(1) a sample database (a Lucene index) containing a few drug names
+
+(2) a sample database (using 2 Lucene indexes) containing a few anatomical
+sites, procedures, and disorders/diseases
+
+These can be used to verify your cTAKES install and to give a small flavor of
+what cTAKES can do, and unlike the bundled UMLS dictionaries, do not require a
+UMLS username or an internet connection.
+
+The programs used to create these Lucene indexes are scripts/java/edu/mayo/bmi
+/dictionarytools/CreateLuceneIndexForExampleDrugs.java and scripts/java/edu/ma
+yo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+To view the contents of a Lucene index, you could use a tool such as Luke.
+
+## Creating your own dictionaries
+
+To create a dictionary yourself, you could download a copy of the UMLS
+Metathesaurus and build upon the program mentioned above to create a Lucene
+index of the desired vocabulary.
+
+Alternatively, you could use a different program in that same package that
+reads from a pipe-delimited file:
+
+scripts/java/edu/mayo/bmi/dictionarytools to create a Lucene index.
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