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From seanfi...@apache.org
Subject svn commit: r1624024 - in /ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary: fast/ fast/ctakes_sno_rx_mem/ fast/example/ fast/example/bsv/ lookup2/Snomed2011ab_ctakesTui/
Date Wed, 10 Sep 2014 15:11:26 GMT
Author: seanfinan
Date: Wed Sep 10 15:11:25 2014
New Revision: 1624024

URL: http://svn.apache.org/r1624024
Log:
Switch to concept database,
Improved Resource xml specifier format
Using subdirectory "fast" to replace "lookup2"

Added:
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/cTakesHsql.xml
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/ctakes_sno_rx_mem/
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiBsv.xml
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTui2Bsv.xml
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTuiBsv.xml
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_bsv.bsv
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_tui_bsv.bsv
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_mixed_bsv.bsv
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_tui_bsv.bsv
Modified:
    ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/cTakesHsql.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/cTakesHsql.xml?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/cTakesHsql.xml
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/cTakesHsql.xml
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<lookupSpecification>
+
+    <dictionaries>
+        <dictionary>
+            <name>UmlsHsqlRareWord</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.JdbcRareWordDictionary</implementationName>
+            <properties>
+                <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
+                <property key="jdbcUrl" value="jdbc:hsqldb:res:org/apache/ctakes/dictionary/fast/ctakes_sno_rx_mem/ctakes_sno_rx_mem"/>
+                <property key="jdbcUser" value="sa"/>
+                <property key="jdbcPass" value=""/>
+                <property key="rareWordTable" value="cui_terms"/>
+                <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser"/>
+                <property key="umlsVendor" value="NLM-6515182895"/>
+                <property key="umlsUser" value="CHANGEME"/>
+                <property key="umlsPass" value="CHANGEME"/>
+            </properties>
+        </dictionary>
+    </dictionaries>
+
+    <conceptFactories>
+        <conceptFactory>
+            <name>UmlsHsqlCuiTable</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
+            <properties>
+                <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
+                <property key="jdbcUrl" value="jdbc:hsqldb:res:org/apache/ctakes/dictionary/fast/ctakes_sno_rx_mem/ctakes_sno_rx_mem"/>
+                <property key="jdbcUser" value="sa"/>
+                <property key="jdbcPass" value=""/>
+                <property key="tuiTable" value="tui"/>
+                <property key="prefTermTable" value="prefTerm"/>
+                <!--<property key="snomedTable" value="snomedct"/>-->
+                <!--<property key="rxNormTable" value="rxnorm"/>-->
+                <!--<property key="icd9Table" value="icd9cm"/>-->
+                <!--<property key="icd10Table" value="icd10pcs"/>-->
+                <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser"/>
+                <property key="umlsVendor" value="NLM-6515182895"/>
+                <property key="umlsUser" value="CHANGEME"/>
+                <property key="umlsPass" value="CHANGEME"/>
+            </properties>
+        </conceptFactory>
+    </conceptFactories>
+
+   <!--  Defines what terms and concepts will be used  -->
+    <dictionaryConceptPairs>
+        <dictionaryConceptPair>
+            <name>cTakesUmls</name>
+            <dictionaryName>UmlsHsqlRareWord</dictionaryName>
+            <conceptFactoryName>UmlsHsqlCuiTable</conceptFactoryName>
+        </dictionaryConceptPair>
+    </dictionaryConceptPairs>
+
+    <!-- PrecisionTermConsumer will only persist only the longest overlapping span of
any semantic group -->
+   <!-- DefaultTermConsumer will persist all spans  -->
+    <rareWordConsumer>
+        <name>Term Consumer</name>
+        <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
+        <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
+        <properties>
+            <property key="codingScheme" value="cTakes"/>
+        </properties>
+    </rareWordConsumer>
+
+</lookupSpecification>

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiBsv.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiBsv.xml?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiBsv.xml
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiBsv.xml
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<lookupSpecification>
+
+    <dictionaries>
+        <dictionary>
+            <name>CustomCuiRareWord</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary</implementationName>
+            <properties>
+                <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_bsv.bsv"/>
+            </properties>
+        </dictionary>
+    </dictionaries>
+
+   <!--  Defines what terms and concepts will be used  -->
+    <dictionaryConceptPairs>
+        <dictionaryConceptPair>
+            <name>CustomPair</name>
+            <dictionaryName>CustomCuiRareWord</dictionaryName>
+        </dictionaryConceptPair>
+    </dictionaryConceptPairs>
+
+    <!-- PrecisionTermConsumer will only persist only the longest overlapping span of
any semantic group -->
+   <!-- DefaultTermConsumer will persist all spans  -->
+    <rareWordConsumer>
+        <name>Term Consumer</name>
+        <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
+        <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
+        <properties>
+            <property key="codingScheme" value="custom"/>
+        </properties>
+    </rareWordConsumer>
+
+</lookupSpecification>

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTui2Bsv.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTui2Bsv.xml?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTui2Bsv.xml
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTui2Bsv.xml
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<lookupSpecification>
+
+    <dictionaries>
+        <dictionary>
+            <name>CustomCuiRareWord</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary</implementationName>
+            <properties>
+                <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_bsv.bsv"/>
+            </properties>
+        </dictionary>
+    </dictionaries>
+
+    <conceptFactories>
+        <conceptFactory>
+            <name>CustomCuiConcept</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory</implementationName>
+            <properties>
+                <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_tui_bsv.bsv"/>
+            </properties>
+        </conceptFactory>
+    </conceptFactories>
+
+    <!--  Defines what terms and concepts will be used  -->
+    <dictionaryConceptPairs>
+        <dictionaryConceptPair>
+            <name>CustomPair</name>
+            <dictionaryName>CustomRareWord</dictionaryName>
+            <conceptFactoryName>CustomCuiConcept</conceptFactoryName>
+        </dictionaryConceptPair>
+    </dictionaryConceptPairs>
+
+    <!-- PrecisionTermConsumer will only persist only the longest overlapping span of
any semantic group -->
+    <!-- DefaultTermConsumer will persist all spans  -->
+    <rareWordConsumer>
+        <name>Term Consumer</name>
+        <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
+        <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
+        <properties>
+            <property key="codingScheme" value="custom"/>
+        </properties>
+    </rareWordConsumer>
+
+</lookupSpecification>

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTuiBsv.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTuiBsv.xml?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTuiBsv.xml
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/CustomCuiTuiBsv.xml
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<lookupSpecification>
+
+    <dictionaries>
+        <dictionary>
+            <name>CustomCuiRareWord</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary</implementationName>
+            <properties>
+                <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv"/>
+            </properties>
+        </dictionary>
+    </dictionaries>
+
+    <conceptFactories>
+        <conceptFactory>
+            <name>CustomCuiConcept</name>
+            <implementationName>org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory</implementationName>
+            <properties>
+                <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv"/>
+            </properties>
+        </conceptFactory>
+    </conceptFactories>
+
+    <!--  Defines what terms and concepts will be used  -->
+    <dictionaryConceptPairs>
+        <dictionaryConceptPair>
+            <name>CustomPair</name>
+            <dictionaryName>CustomRareWord</dictionaryName>
+            <conceptFactoryName>CustomCuiConcept</conceptFactoryName>
+        </dictionaryConceptPair>
+    </dictionaryConceptPairs>
+
+    <!-- PrecisionTermConsumer will only persist only the longest overlapping span of
any semantic group -->
+    <!-- DefaultTermConsumer will persist all spans  -->
+    <rareWordConsumer>
+        <name>Term Consumer</name>
+        <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
+        <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
+        <properties>
+            <property key="codingScheme" value="custom"/>
+        </properties>
+    </rareWordConsumer>
+
+</lookupSpecification>

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_bsv.bsv
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_bsv.bsv?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_bsv.bsv
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_bsv.bsv
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,22 @@
+1|ctakes
+1|ctakes application
+// line comments can start with double-slash
+2|new dictionary lookup
+2|dictionary lookup, new
+2|fast dictionary lookup
+2|dictionary-lookup-fast
+# line comments can start with hash
+3|text tokenization is automatic, for bsv
+3|for .bsv files, text-tokenization is done upon loading
+3|There's no need to WORRY about matching the cTakes token scheme
+4|the entire bsv dictionary is loaded, then rare words are determined
+4|the rare-word indexing is used for custom bsv just like umls hsql
+5|CUIs must be 1-7 digits characters.  First-character "C" is optional
+C5|Note that C5, C0000005 5, 05, and 005 are translated as the same cui
+6|The bsv loader will detect 2 or 3 or 4 columns
+6|2 columns are parsed as CUI , Text if set as a dictionary
+6|2 columns are parsed as CUI , TUI if set as a concept factory
+7|3 columns are parsed as CUI , TUI , Text if set as a dictionary and/or concept factory
+8|4 columns are parsed as CUI , TUI , Text , Preferred Term if set as a dictionary and/or
concept factory
+
+

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_tui_bsv.bsv
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_tui_bsv.bsv?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_tui_bsv.bsv
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_cui_tui_bsv.bsv
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,22 @@
+1|1|ctakes
+1|1|ctakes application
+// line comments can start with double-slash
+2|3|new dictionary lookup
+2|3|dictionary lookup, new
+2|3|fast dictionary lookup
+2|3|dictionary-lookup-fast
+# line comments can start with hash
+3|5|text tokenization is automatic, for bsv
+3|5|for .bsv files, text-tokenization is done upon loading
+3|5|There's no need to WORRY about matching the cTakes token scheme
+4|5|the entire bsv dictionary is loaded, then rare words are determined
+4|5|the rare-word indexing is used for custom bsv just like umls hsql
+5|5|CUIs must be 1-7 digits.  First-character "C" is optional
+C5|5|Note that C5, C0000005 5, 05, and 005 are translated as the same cui
+6|5|The bsv loader will detect 2 or 3 or 4 columns
+6|5|2 columns are parsed as CUI , Text if set as a dictionary
+6|5|2 columns are parsed as CUI , TUI if set as a concept factory
+7|5|3 columns are parsed as CUI , TUI , Text if set as a dictionary and/or concept factory
+8|5|4 columns are parsed as CUI , TUI , Text , Preferred Term if set as a dictionary and/or
concept factory
+9|5|TUIs must be 1-3 digits.  First-character "T" is optional
+10|T5|Note that T5, T005 5, 05, and 005 are translated as the same tui

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_mixed_bsv.bsv
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_mixed_bsv.bsv?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_mixed_bsv.bsv
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_mixed_bsv.bsv
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,23 @@
+1|1|ctakes
+1||ctakes application
+// line comments can start with double-slash
+2|3|new dictionary lookup|dictionary-lookup-fast
+2||dictionary lookup, new
+2||fast dictionary lookup
+2||dictionary-lookup-fast
+# line comments can start with hash
+3|5|text tokenization is automatic, for bsv|Easy Tokenization
+3||for .bsv files, text-tokenization is done upon loading
+3||There's no need to WORRY about matching the cTakes token scheme
+4|||Automatic Rare Word Detection
+4|5|the entire bsv dictionary is loaded, then rare words are determined
+4||the rare-word indexing is used for custom bsv just like umls hsql
+5|5|CUIs must be 1-7 digits.  First-character "C" is optional
+C5|T5|Note that C5, C0000005 5, 05, and 005 are translated as the same cui
+6|5|The bsv loader will detect 2 or 3 or 4 columns
+6||2 columns are parsed as CUI , Text if set as a dictionary
+6||2 columns are parsed as CUI , TUI if set as a concept factory
+7||3 columns are parsed as CUI , TUI , Text if set as a dictionary and/or concept factory
+8||4 columns are parsed as CUI , TUI , Text , Preferred Term if set as a dictionary and/or
concept factory
+9|5|TUIs must be 1-3 digits.  First-character "T" is optional
+10|T5|Note that T5, T005 5, 05, and 005 are translated as the same tui

Added: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_tui_bsv.bsv
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_tui_bsv.bsv?rev=1624024&view=auto
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_tui_bsv.bsv
(added)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/fast/example/bsv/custom_tui_bsv.bsv
Wed Sep 10 15:11:25 2014
@@ -0,0 +1,10 @@
+1|1
+// line comments can start with double-slash
+2|3
+# line comments can start with hash
+3|5
+4|5
+C5|5
+6|5
+9|5
+10|T5

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml?rev=1624024&r1=1624023&r2=1624024&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
Wed Sep 10 15:11:25 2014
@@ -25,22 +25,33 @@
       <!-- typeId 0 is the cTakes constant for unknown - let the consumer take care of
typing  -->
       <dictionary id="cTakes" externalResourceKey="cTakesSnomed" caseSensitive="false"
typeId="0">
          <implementation>
-            <rareWordUmls tableName="cTakes_umls"/>
+            <rareWordUmls tableName="cTakes_umls"  umlsUrl="https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser"
+                          vendor="NLM-6515182895" user="CHANGEME" password="CHANGEME"/>
          </implementation>
       </dictionary>
    </rareWordDictionaries>
 
-   <!-- PrecisionTermConsumer will only persist only the longest overlapping span of any
semantic group -->
-   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer">
-      <properties>
-         <property key="codingScheme" value="cTakes"/>
-      </properties>
-   </rareWordConsumer>
+    <!-- JdbcConceptFactory populates concept info from a database -->
+    <conceptFactory id="cTakes" externalResourceKey="cTakesSnomed">
+        <implementation>
+            <!-- cuiTables = JdbcConceptFactory; populates concept info from a database
-->
+            <!--<cuiTables tui="TUI" snomedct="SNOMEDCT" rxNorm="RXNORM" icd9cm="ICD9CM"
icd10pcs="ICD10PCS" preferredTerm="PREFTERM"/>-->
+            <primitiveConcept tui="TUI" preferredTerm="PREFTERM"/>
+        </implementation>
+    </conceptFactory>
+
+    <!-- PrecisionTermConsumer will only persist only the longest overlapping span of
any semantic group -->
+   <!--<rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer">-->
+      <!--<properties>-->
+         <!--<property key="codingScheme" value="cTakes"/>-->
+      <!--</properties>-->
+   <!--</rareWordConsumer>-->
 
    <!-- DefaultTermConsumer will persist all spans  -->
-<!--   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer">
+   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer">
       <properties>
          <property key="codingScheme" value="cTakes"/>
       </properties>
-   </rareWordConsumer>  -->
+   </rareWordConsumer>
+
 </lookupSpecification>



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