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From Phan Hồng Phúc <phanhongphu...@gmail.com>
Subject Re: Clinical Element Model normalization component
Date Wed, 10 Feb 2016 09:10:53 GMT
Hi Guergana,

I have already added the dictionary to the resources folder.
How can I check IdentifiedAnnotations? (Sorry I am first time use cTakes
library :-) )

Here is the log I copied from console:

log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is  [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
10 Feb 2016 16:01:14  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
E:\workspace\metamap_project\apache-ctakes-3.2.2\resources\org\apache\ctakes\lvg\data\config\lvg.properties
10 Feb 2016 16:01:14  INFO LvgCmdApiResourceImpl -   config file absolute
path =
E:\workspace\metamap_project\apache-ctakes-3.2.2\resources\org\apache\ctakes\lvg\data\config\lvg.properties
10 Feb 2016 16:01:14  INFO LvgCmdApiResourceImpl - cwd =
E:\workspace\metamap_project\apache-ctakes-3.2.2
10 Feb 2016 16:01:14  INFO LvgCmdApiResourceImpl - cd
E:\workspace\metamap_project\apache-ctakes-3.2.2\resources\org\apache\ctakes\lvg\
10 Feb 2016 16:01:15  INFO LvgCmdApiResourceImpl - cd
E:\workspace\metamap_project\apache-ctakes-3.2.2
10 Feb 2016 16:01:15  INFO ClearNLPDependencyParserAE - using Morphy
analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
10 Feb 2016 16:01:27  INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
10 Feb 2016 16:01:28  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
10 Feb 2016 16:01:28  INFO ConstituencyParser - Initializing parser...
10 Feb 2016 16:01:33  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
10 Feb 2016 16:01:33  INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
10 Feb 2016 16:01:33  INFO DrugMentionAnnotator - Finite state machines
loaded.
10 Feb 2016 16:01:33  INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
10 Feb 2016 16:01:34  INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
10 Feb 2016 16:01:34  INFO AbstractJCasTermAnnotator - Exclusion tagset
loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN
VBP VBZ WDT WP WPS WRB
10 Feb 2016 16:01:34  INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
10 Feb 2016 16:01:34  INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
E:\workspace\metamap_project\apache-ctakes-3.2.2\resources\org\apache\ctakes\dictionary\lookup\fast\cTakesHsql.xml
10 Feb 2016 16:01:34  INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user phanhongphucit:
...................
10 Feb 2016 16:01:41  INFO UmlsUserApprover -   UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user phanhongphucit
has been validated
10 Feb 2016 16:01:41  INFO JdbcConnectionFactory - Connecting to
jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx:
..........
10 Feb 2016 16:01:44  INFO JdbcConnectionFactory -  Database connected
Loading configuration.
Loading feature templates.
Loading model:
.
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
...
Loading model:
.
Loading model:
...
.
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
................................
Loading model:
.............................
10 Feb 2016 16:01:49  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
10 Feb 2016 16:01:49  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
10 Feb 2016 16:01:49  INFO StatusContextAnalyzer - initBoundaryData()
called for ContextInitializer
10 Feb 2016 16:01:50  INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
10 Feb 2016 16:02:38  INFO SentenceDetector - Starting processing.
10 Feb 2016 16:02:38  INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
10 Feb 2016 16:02:38  INFO LvgAnnotator - process(JCas)
10 Feb 2016 16:02:39  INFO ContextDependentTokenizerAnnotator -
process(JCas)
10 Feb 2016 16:02:39  INFO POSTagger - process(JCas)
10 Feb 2016 16:02:39  INFO Chunker -  process(JCas)
10 Feb 2016 16:02:39  INFO ChunkAdjuster -  process(JCas)
10 Feb 2016 16:02:39  INFO ChunkAdjuster -  process(JCas)
10 Feb 2016 16:02:39  INFO AbstractJCasTermAnnotator - Starting processing
10 Feb 2016 16:02:39  INFO AbstractJCasTermAnnotator - Finished processing
10 Feb 2016 16:02:39  INFO DrugMentionAnnotator - process(JCas)
10 Feb 2016 16:02:39  INFO MaxentParserWrapper - Started processing: null
10 Feb 2016 16:02:39  INFO MaxentParserWrapper - Done parsing: null

Thank you,
- Phúc

2016-02-10 2:21 GMT+07:00 Savova, Guergana <
Guergana.Savova@childrens.harvard.edu>:

> Hi Phuc,
> Did you create a dictionary to run your pipeline with?
> Did you check under IdentifiedAnnotations where there are annotations of
> type Drugs?
> --Guergana
>
>
> -----Original Message-----
> From: Phan Hồng Phúc [mailto:phanhongphucit@gmail.com]
> Sent: Tuesday, February 9, 2016 2:19 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Element Model normalization component
>
> Hi all,
>
> I try to run the sample to get the drug name.
> Let me describe my steps:
> - runctakesCVD.bat
> - Load AE:
>
> apache-ctakes-3.2.2\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor
> - Add sample text: "*He is taking 500mg of tylenol, twice a day"*
> *- *After run, I see a list of result but all type
> org.apache.ctakes.drugner.type.* are [0]
>
> I think it should contain at least drug name "tylenol" in the result.
>
> Do I miss something?
>
> Thank you,
> - Phúc
>

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