Hi Sean
Thanks Again!
I am seeing few more FP like MEN :
SENTENCE: MEN
NN
|======|
Disorder
C0027662
|======|
Drug
C0127527
Where as it could have been matched to :
Meta Mapping (1000):
1000 C0025266:Men (Male population group)
2) Also is there any way round to match based on spelling mistakes. like
advill ==> advil
neplasm ==> neoplasm
3) Can we all concepts from MRCONSO into fast matching dictionary.
On Wed, Jan 25, 2017 at 10:12 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Shahid,
>
>
>
> I tested LVG on “levels” and it didn’t produce an equivalent singular
> form. I don’t know of any special lvg parameters that will toggle this on
> and off – as far as I know it should always attempt it for nouns. Because
> this may happen quite a bit I started thinking on an alternative solution …
> but may not get to it for a while and when I do I’ll still need to run some
> tests to make sure it works.
>
>
>
> Andrey Kurdumov recently made an update for ctakes to use LVG 2016
> (cheers!). The current version is fairly old and the 2016 may very well
> perform better. I have pasted his email below.
>
>
>
> As I promise, I udpate cTakes to support LVG version 2016 year.
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=
> IJWxluJDIVhugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e=
>
>
>
> Please take a look.
>
> In the github following modifications to current version of cTakes
>
> - Removed two large files to make project fit GitHub restrictions.
>
> - Some very small cleanup which placed in separate commit.
>
> - Some fixes to ytex related tests, that's was required for me to pass mvn
> install command.
>
>
>
> Assumptions:
>
> - User should update ctakesnormx and other databases from HSQLdb 1.8 to
> HSQLDB 2.3.4
>
>
>
>
>
>
>
> *From:* shahid ashraf [mailto:sha...@trialx.com]
> *Sent:* Wednesday, January 25, 2017 2:11 AM
>
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks sean for this insightful information. This is of great help.(i am
> newbie to ctakes and also come from python background.)
>
> I tested on the Fast version. Is it so that ctakes LVG is not currently
> adding plurals to the terms. Because in logs i see that LVG is being setup
> before processing the docs in CVD.
>
> I guess below logs show ctakes is using LVG:
>
>
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> Lvg with config file = /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/data/
> config/lvg.properties
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - config file absolute
> path = /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/data/
> config/lvg.properties
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cwd =
> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/workspace/ctakes/ctakes-
> dictionary-lookup/resources/org/apache/ctakes/lvg/
>
> 25 Jan 2017 12:31:40 INFO LvgCmdApiResourceImpl - cd
> /Users/shahid/projects/workspace/ctakes/ctakes-clinical-pipeline
>
> 25 Jan 2017 12:31:40 INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true
>
> Loading configuration.
>
> Loading feature templates.
>
> Loading lexica.
>
> Loading model:
>
> ............................................................
> ............................
>
> 25 Jan 2017 12:31:54 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
> 25 Jan 2017 12:31:55 INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
>
> 25 Jan 2017 12:31:55 INFO ConstituencyParser - Initializing parser...
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using left , right scope
> sizes: 7 , 7
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context analyzer:
> org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
>
> 25 Jan 2017 12:31:59 INFO NegationContextAnalyzer - initBoundaryData()
> called for ContextInitializer
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context consumer:
> org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using lookup window type:
> org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using focus type:
> org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
>
> 25 Jan 2017 12:31:59 INFO ContextAnnotator - Using context type:
> org.apache.ctakes.typesystem.type.syntax.BaseToken
>
> 25 Jan 2017 12:31:59 INFO DrugMentionAnnotator - Finite state machines
> loaded.
>
> 25 Jan 2017 12:31:59 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Exclusion tagset
> loaded: CC CD EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP
> VBZ WDT WP WPS WRB
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
>
> 25 Jan 2017 12:32:00 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/custom_
> appliedvocab.xml
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - saxBuilder had
> build doc
>
> FILEPATH: [Document: No DOCTYPE declaration, Root is [Element:
> <lookupSpecification/>]]
>
> 25 Jan 2017 12:32:00 INFO JdbcRareWordDictionary - Connected to cui and
> term table CUI_TERMS
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - RareWordDictionary
> parseDictionaries Done...
>
> [Element: <conceptFactories/>]
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
> parseConceptFactories...
>
> 25 Jan 2017 12:32:00 INFO DictionaryDescriptorParser - Started
> parseConceptFactories... Collection
>
>
>
> Also in FASTAGGREGATE PIPELINE Desc i see
>
> <flowConstraints>
>
> <fixedFlow>
>
> <node>SimpleSegmentAnnotator</node>
>
> <node>SentenceDetectorAnnotator</node>
>
> <node>TokenizerAnnotator</node>
>
> * <node>LvgAnnotator</node>*
>
> <node>ContextDependentTokenizerAnnotator</node>
>
> <node>POSTagger</node>
>
> <!-- <node>ClearPOSTagger</node> -->
>
> <node>Chunker</node>
>
> <node>AdjustNounPhraseToIncludeFollowingNP</node>
>
> <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
>
> <node>LookupWindowAnnotator</node>
>
> <node>DictionaryLookupAnnotatorDB</node>
>
> <node>DependencyParser</node>
>
> ...
>
> </fixedFlow>
>
>
>
>
>
> Is there any setting that will let LVG generate plurals.
>
>
>
> On Wed, Jan 25, 2017 at 1:08 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
> You will definitely find instances where the old dictionary finds terms
> but the fast does not, and vice-versa. The fast lookup uses a more concise
> dictionary, and the concepts that you noted are probably not in it. There
> is another thread between myself and Pratik Agarwal (last week in fact) on
> exactly the topic of drugs identified generically or with dose, route,
> form, etc. That may be why you don’t see everolimus 2.5 mg specifically.
>
> Everolimus is in the dictionary by itself:
>
> sql> select * from cui_terms where text like '%everolimus%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ---------- ----------
>
> 541315 0 1 everolimus everolimus
>
>
>
> The reason why everolimus was not identified by itself is because it was
> given the part of speech “DT” (Determiner), which is specified as unwanted
> for lookup. In my test with “… given everolimus 2.5 MG …”:
>
> WordToken
>
> begin
>
> 12
>
> end
>
> 16
>
> tokenNumber
>
> 2
>
> partOfSpeech
>
> VBD
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> WordToken
>
> begin
>
> 17
>
> end
>
> 27
>
> tokenNumber
>
> 3
>
> partOfSpeech
>
> DT
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> MeasurementAnnotation
>
> begin
>
> 28
>
> end
>
> 34
>
> id
>
> 0
>
> typeID
>
> 0
>
> discoveryTechnique
>
> 0
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
>
>
> “DT” normally is assigned to things like “the, a, these” and at some
> point the community decided that words with the DT part of speech should
> not be considered as candidates for dictionary lookup.
> http://www.clips.ua.ac.be/pages/mbsp-tags
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.clips.ua.ac.be_pages_mbsp-2Dtags&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=3k7SCH8Gvj_palkdWwWeKGysBHTV_K5itUG2DE4icAI&s=xwP78R729SFVEwbCNa_af452uzXvIik2Ob4SYQyNPHw&e=>
>
> The default exclusion parts of speech are:
>
>
> “VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB”
>
> To change this, set the parameter “exclusionTags” to this string without
> DT.
>
>
>
> As for “higher testosterone levels”, are you running the LVG (Lexical
> Variant Generator) module? “testosterone level” is in the dictionary, but
> the plural “testosterone levels” is not. This is done on purpose to keep
> the database small. The old dictionary may not have the same tactic.
>
> sql> select * from cui_terms where text like 'testosterone level%';
>
> CUI RINDEX TCOUNT TEXT RWORD
>
> ------ ------ ------ ------------------ ------------
>
> 523912 0 2 testosterone level testosterone
>
>
>
> The LVG module –should- add the plural as a variant and the lookup module
> will use that variant for lookup. The dictionary module (and others) does
> not stand on its own – its success depends upon the proper output of
> previous modules in the pipeline. When I test with “… higher testosterone
> level …” (without LVG) it does find what you are looking for:
>
> WordToken
>
> begin
>
> 18
>
> end
>
> 24
>
> tokenNumber
>
> 4
>
> partOfSpeech
>
> JJR
>
> capitalization
>
> 0
>
> numPosition
>
> 0
>
> ProcedureMention
>
> begin
>
> 25
>
> end
>
> 43
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 104957004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0523912
>
> tui
>
> T059
>
> preferredText
>
> Testosterone measurement
>
> typeID
>
> 5
>
> discoveryTechnique
>
> 1
>
> polarity
>
> 0
>
> uncertainty
>
> 0
>
> conditional
>
> false
>
> generic
>
> false
>
> historyOf
>
> 0
>
> MedicationMention
>
> begin
>
> 25
>
> end
>
> 37
>
> id
>
> 0
>
> codingScheme
>
> SNOMEDCT
>
> code
>
> 109033004
>
> score
>
> 0.0
>
> disambiguated
>
> false
>
> cui
>
> C0039601
>
> tui
>
> T121
>
> preferredText
>
> Testosterone
>
> codingScheme
>
>
>
> I just ran through with LVG and LVG does not form “level” from “levels”.
>
>
>
>
> I hope that helps,
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:sha...@trialx.com]
> *Sent:* Tuesday, January 24, 2017 10:17 AM
>
>
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Hi Sean
>
>
>
> I am testing the stuff on the fast and AggregratePlainTextUMLSProcessor(slow)
> . I found that one of the drug everolimus 2.5 mg is not found by the
> fast version. it is actually in RXNORM of my MRCONSO.RRF file.
>
> C2920405|ENG|P|L9442487|PF|S11732013|Y|A18083986|3277628|
> 998191||RXNORM|SBD|998191|*everolimus 2.5 MG* Oral Tablet
> [Afinitor]|0|N|4352|. Let me know if you have any inputs on this.
>
> Also other case is :
>
> SENTENCE: higher testosterone levels
>
> JJR NN NNS
>
> |==========|
>
> Procedure
>
> C0202227
>
> C0523912
>
> |==========|
>
> Drug
>
> C0039601
>
> AggregratePlainTextUMLSProcessor is able to find from higher testosterone
> levels:
>
> *testosterone levels*
>
> <refsem:UmlsConcept xmi:id="167" codingScheme="SNOMED" code="104957004"
> oid="104957004#SNOMED" score="0.0" disambiguated="false" cui="C0523912"
> tui="T059"/>
>
> C0523912|ENG|S|L0865889|PF|S1044605|Y|A3209597|1219087010|104957004||SNOMEDCT_US|SY|104957004|Testosterone
> level|9|N|256|
>
> I am not able to understand why fast version is not able to do so.
>
>
>
> MoreOver in comparison to Metamap, we are not able to do this.
>
> Phrase: higher testosterone levels
>
> Meta Mapping (966):
>
> 966 C1295653:High testosterone level (Increased testosterone level)
> [Finding]
>
>
>
> On Tue, Jan 24, 2017 at 8:19 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> Hi Shahid,
>
>
>
> I’m glad that the fix worked!
>
> Unfortunately, the fast dictionary format will not work with the old
> Dictionary Lookup Module that is used by AggregratePlainTextUMLSProcessor
>
> You can manually create an updated dictionary for the older module, but it
> is more involved.
>
> In our tests and those done by others the new “fast” lookup has as good or
> better accuracy depending upon the test corpus. Plus it is runs in 1/500
> th the time. I recommend that you stick to it.
>
>
>
> Sean
>
>
>
> *From:* shahid ashraf [mailto:sha...@trialx.com]
> *Sent:* Tuesday, January 24, 2017 5:50 AM
> *To:* Finan, Sean
> *Cc:* dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal
>
>
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Thanks Sean
>
>
>
> That was the case for not finding the class. there were space in the xml
> generated by dictionary-gui.
>
> Also i am curious how we can use new umls with normal
> AggregratePlainTextUMLSProcessor.
>
>
>
>
>
> On Mon, Jan 23, 2017 at 9:36 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> Ah – there might be an erroneous space in the classname.
>
>
>
> Go to your dictionary settings xml. In the line:
>
> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory</implementationName>
>
>
>
> Look for a space between “JdbcConceptFactory” and “</implementationName>”
>
> If you see a space, remove it.
>
>
>
> It looks like I introduced this bug a few weeks ago.
>
>
>
> Thanks,
>
> Sean
>
>
>
>
>
> *From:* shahid ashraf [mailto:sha...@trialx.com]
> *Sent:* Saturday, January 21, 2017 1:42 PM
> *To:* dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; pratik
> agarwal
> *Subject:* Re: Ctakes Dictionary Gui
>
>
>
> Have put username and password (umls) in custom.xml as well. Still getting
> this error:
>
> 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd.
> MainFrame.handleException(526): SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
> AnalysisEngineFactory_impl.java:94)
>
> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
> CompositeResourceFactory_impl.java:62)
>
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:387)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> setup(ASB_impl.java:254)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initASB(AggregateAnalysisEngine_impl.java:431)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initialize(AggregateAnalysisEngine_impl.java:185)
>
> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
> AnalysisEngineFactory_impl.java:94)
>
> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
> CompositeResourceFactory_impl.java:62)
>
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:354)
>
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>
> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(
> MainFrame.java:476)
>
> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.
> actionPerformed(AnnotatorOpenEventHandler.java:52)
>
> at javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:2022)
>
> at javax.swing.AbstractButton$Handler.actionPerformed(
> AbstractButton.java:2346)
>
> at javax.swing.DefaultButtonModel.fireActionPerformed(
> DefaultButtonModel.java:402)
>
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>
> at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:833)
>
> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
>
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.
> mouseReleased(BasicMenuItemUI.java:877)
>
> at java.awt.Component.processMouseEvent(Component.java:6525)
>
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
>
> at java.awt.Component.processEvent(Component.java:6290)
>
> at java.awt.Container.processEvent(Container.java:2234)
>
> at java.awt.Component.dispatchEventImpl(Component.java:4881)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2292)
>
> at java.awt.Component.dispatchEvent(Component.java:4703)
>
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
>
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
>
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2278)
>
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
>
> at java.awt.Component.dispatchEvent(Component.java:4703)
>
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
>
> at java.awt.EventQueue.access$500(EventQueue.java:97)
>
> at java.awt.EventQueue$3.run(EventQueue.java:709)
>
> at java.awt.EventQueue$3.run(EventQueue.java:703)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:75)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:86)
>
> at java.awt.EventQueue$4.run(EventQueue.java:731)
>
> at java.awt.EventQueue$4.run(EventQueue.java:729)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:75)
>
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(
> EventDispatchThread.java:201)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(
> EventDispatchThread.java:116)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(
> EventDispatchThread.java:105)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by:
> org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
>
>
> On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sha...@trialx.com> wrote:
>
> Hi I was able to run and produce the new custom umls files. and where put
> under ctakes binary (not dev).
>
>
>
> I changed the name under apache-ctakes-3.2.2/
> desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/
> UmlsLookupAnnotator.xml
>
>
>
> <name>DictionaryDescriptorFile</name>
>
> <description/>
>
> <fileResourceSpecifier>
>
> <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/
> custom.xml</fileUrl>
>
>
>
> when running AggregatePlantextFastUmlsProcessor.xml I am getting
> following error (not when using old org/apache/ctakes/
> dictionary/lookup/fast/cTakesHsql.xml)
>
>
>
> 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class "org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .DefaultJCasTermAnnotator" failed. (Descriptor:
> file:/usr/local/apache-ctakes-3.2.2/desc/ctakes-dictionary-
> lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
>
> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
> AnalysisEngineFactory_impl.java:94)
>
> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
> CompositeResourceFactory_impl.java:62)
>
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:387)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> setup(ASB_impl.java:254)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initASB(AggregateAnalysisEngine_impl.java:431)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initialize(AggregateAnalysisEngine_impl.java:185)
>
> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
> AnalysisEngineFactory_impl.java:94)
>
> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
> CompositeResourceFactory_impl.java:62)
>
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:354)
>
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>
> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(
> MainFrame.java:476)
>
> at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.
> actionPerformed(AnnotatorOpenEventHandler.java:52)
>
> at javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:2022)
>
> at javax.swing.AbstractButton$Handler.actionPerformed(
> AbstractButton.java:2346)
>
> at javax.swing.DefaultButtonModel.fireActionPerformed(
> DefaultButtonModel.java:402)
>
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>
> at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:833)
>
> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
>
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.
> mouseReleased(BasicMenuItemUI.java:877)
>
> at java.awt.Component.processMouseEvent(Component.java:6525)
>
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
>
> at java.awt.Component.processEvent(Component.java:6290)
>
> at java.awt.Container.processEvent(Container.java:2234)
>
> at java.awt.Component.dispatchEventImpl(Component.java:4881)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2292)
>
> at java.awt.Component.dispatchEvent(Component.java:4703)
>
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
>
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
>
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2278)
>
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
>
> at java.awt.Component.dispatchEvent(Component.java:4703)
>
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
>
> at java.awt.EventQueue.access$500(EventQueue.java:97)
>
> at java.awt.EventQueue$3.run(EventQueue.java:709)
>
> at java.awt.EventQueue$3.run(EventQueue.java:703)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:75)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:86)
>
> at java.awt.EventQueue$4.run(EventQueue.java:731)
>
> at java.awt.EventQueue$4.run(EventQueue.java:729)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(
> ProtectionDomain.java:75)
>
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(
> EventDispatchThread.java:201)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(
> EventDispatchThread.java:116)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(
> EventDispatchThread.java:105)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>
> ... 55 more
>
> Caused by:
> org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key
> Unknown class org.apache.ctakes.dictionary.lookup2.concept.
> JdbcConceptFactory
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:255)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactories(
> DictionaryDescriptorParser.java:226)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.
> java:133)
>
> at org.apache.ctakes.dictionary.lookup2.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup2.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=LaGFaTnSoKexqlXkoxOvEuIP-e7Ktmu3vKI0ZckDzcA&s=WaHWxD5eLKHj4eMgOkvTvzUiNAHAZybtjddO0KE2jgI&e=>
> .AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
>
> ... 56 more
>
> Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary.
> lookup2.concept.JdbcConceptFactory
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser.
> java:253)
>
> ... 59 more
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
>
>
>
>
> --
>
> with Regards
>
> Shahid Ashraf
>
--
with Regards
Shahid Ashraf
