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Posted to dev@ctakes.apache.org by Phan Hồng Phúc <ph...@gmail.com> on 2016/02/08 19:19:01 UTC
Clinical Element Model normalization component
Hi,
I could not find the annotation for Clinical Element Model normalization
module on apache-ctakes-3.2.2/desc
[image: Hình ảnh nội tuyến 1]
Could you please tell me where it is?
Thanks!
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
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
>
RE: Clinical Element Model normalization component
Posted by "Savova, Guergana" <Gu...@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
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
Hi Jessica,
I start from MedicationMention now.
Thank you,
- Phúc
2016-02-10 21:27 GMT+07:00 Jessica Glover <gl...@gmail.com>:
> Hi,
> I saw that it does come with DrugNER, but I also find that isn't picking up
> Tylenol as an ner type annotation. I'm curious to know whether DrugNER
> worked prior to 3.2 . I will keep digging. In the meantime I hope you find
> MedicationMention in the IdentifiedAnnotations. I don't think the
> attributes like dosage, etc. get populated, but it does pick up Tylenol for
> me.
>
> - Jessica
> On Feb 10, 2016 4:30 AM, "Phan Hồng Phúc" <ph...@gmail.com>
> wrote:
>
> > Thanks Jessica, looking forward to you..
> > Just an information that from this email
> >
> >
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201508.mbox/%3CCOL130-W826156991F6C8E4085DA7AFB7D0@phx.gbl%3E
> > Chenpei said that AggregatePlaintextFastUMLSProcessor.xml should already
> > have
> > the Drug NER included.
> >
> > Regards,
> > - Phúc
> >
> >
> >
> >
> > 2016-02-10 3:51 GMT+07:00 Jessica Glover <gl...@gmail.com>:
> >
> > > I believe you need to add an annotator like DrugAggregateCDAProcessor
> to
> > > the pipeline to get the annotations you seek. I will investigate and
> > write
> > > more soon.
> > >
> > > - Jessica G.
> > > On Feb 9, 2016 2:31 PM, "Miller, Timothy" <
> > > Timothy.Miller@childrens.harvard.edu> wrote:
> > >
> > > > I'm not that familiar with that module but I can confirm that I was
> > able
> > > > to replicate your output on this example.
> > > > If it helps at all the MedicationMention type does have a span for
> the
> > > > tylenol mention, but obviously doesn't help with all the dosage,
> route,
> > > > etc. information you might want.
> > > > Hopefully one of the devs/maintainers of that module will have some
> > idea.
> > > > Tim
> > > >
> > > >
> > > > On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > > > > 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
> > > > >
> > > >
> > > >
> > >
> >
>
Re: Clinical Element Model normalization component
Posted by Jessica Glover <gl...@gmail.com>.
Hi,
I saw that it does come with DrugNER, but I also find that isn't picking up
Tylenol as an ner type annotation. I'm curious to know whether DrugNER
worked prior to 3.2 . I will keep digging. In the meantime I hope you find
MedicationMention in the IdentifiedAnnotations. I don't think the
attributes like dosage, etc. get populated, but it does pick up Tylenol for
me.
- Jessica
On Feb 10, 2016 4:30 AM, "Phan Hồng Phúc" <ph...@gmail.com>
wrote:
> Thanks Jessica, looking forward to you..
> Just an information that from this email
>
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201508.mbox/%3CCOL130-W826156991F6C8E4085DA7AFB7D0@phx.gbl%3E
> Chenpei said that AggregatePlaintextFastUMLSProcessor.xml should already
> have
> the Drug NER included.
>
> Regards,
> - Phúc
>
>
>
>
> 2016-02-10 3:51 GMT+07:00 Jessica Glover <gl...@gmail.com>:
>
> > I believe you need to add an annotator like DrugAggregateCDAProcessor to
> > the pipeline to get the annotations you seek. I will investigate and
> write
> > more soon.
> >
> > - Jessica G.
> > On Feb 9, 2016 2:31 PM, "Miller, Timothy" <
> > Timothy.Miller@childrens.harvard.edu> wrote:
> >
> > > I'm not that familiar with that module but I can confirm that I was
> able
> > > to replicate your output on this example.
> > > If it helps at all the MedicationMention type does have a span for the
> > > tylenol mention, but obviously doesn't help with all the dosage, route,
> > > etc. information you might want.
> > > Hopefully one of the devs/maintainers of that module will have some
> idea.
> > > Tim
> > >
> > >
> > > On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > > > 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
> > > >
> > >
> > >
> >
>
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
Thanks Jessica, looking forward to you..
Just an information that from this email
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201508.mbox/%3CCOL130-W826156991F6C8E4085DA7AFB7D0@phx.gbl%3E
Chenpei said that AggregatePlaintextFastUMLSProcessor.xml should already have
the Drug NER included.
Regards,
- Phúc
2016-02-10 3:51 GMT+07:00 Jessica Glover <gl...@gmail.com>:
> I believe you need to add an annotator like DrugAggregateCDAProcessor to
> the pipeline to get the annotations you seek. I will investigate and write
> more soon.
>
> - Jessica G.
> On Feb 9, 2016 2:31 PM, "Miller, Timothy" <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> > I'm not that familiar with that module but I can confirm that I was able
> > to replicate your output on this example.
> > If it helps at all the MedicationMention type does have a span for the
> > tylenol mention, but obviously doesn't help with all the dosage, route,
> > etc. information you might want.
> > Hopefully one of the devs/maintainers of that module will have some idea.
> > Tim
> >
> >
> > On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > > 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
> > >
> >
> >
>
Re: Clinical Element Model normalization component
Posted by Jessica Glover <gl...@gmail.com>.
I believe you need to add an annotator like DrugAggregateCDAProcessor to
the pipeline to get the annotations you seek. I will investigate and write
more soon.
- Jessica G.
On Feb 9, 2016 2:31 PM, "Miller, Timothy" <
Timothy.Miller@childrens.harvard.edu> wrote:
> I'm not that familiar with that module but I can confirm that I was able
> to replicate your output on this example.
> If it helps at all the MedicationMention type does have a span for the
> tylenol mention, but obviously doesn't help with all the dosage, route,
> etc. information you might want.
> Hopefully one of the devs/maintainers of that module will have some idea.
> Tim
>
>
> On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > 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
> >
>
>
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
Thank you,
- Phúc
2016-02-10 21:09 GMT+07:00 Miller, Timothy <
Timothy.Miller@childrens.harvard.edu>:
> Yes it is org.apache.ctakes.typesystem.type.textsem.MedicationMention
> Tim
>
>
> On 02/10/2016 04:20 AM, Phan Hồng Phúc wrote:
> > Hi Tim,
> >
> > Could you provide me the full pakage name of annotation type which
> > recognize the 'tylenol' name?
> > Here are the list of annotation drug type I got, it does not contains
> > MedicationMention:
> >
> > - org.apache.ctakes.drugner.type.ChunkAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.DecimalStrengthAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.DosagesAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.DrugMentionAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.DurationAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.FormAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.FractionStrengthAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.FrequencyAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.FrequencyUnitAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.RangeStrengthAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.RouteAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.StrengthAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.StrengthUnitAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.SubSectionAnnotation [0]
> >
> >
> > - org.apache.ctakes.drugner.type.SuffixStrengthAnnotation [0]
> >
> > Thank you,
> > - Phúc
> >
> >
> > 2016-02-10 2:31 GMT+07:00 Miller, Timothy <
> > Timothy.Miller@childrens.harvard.edu>:
> >
> >> I'm not that familiar with that module but I can confirm that I was able
> >> to replicate your output on this example.
> >> If it helps at all the MedicationMention type does have a span for the
> >> tylenol mention, but obviously doesn't help with all the dosage, route,
> >> etc. information you might want.
> >> Hopefully one of the devs/maintainers of that module will have some
> idea.
> >> Tim
> >>
> >>
> >> On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> >>> 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
> >>>
> >>
>
>
Re: Clinical Element Model normalization component
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Yes it is org.apache.ctakes.typesystem.type.textsem.MedicationMention
Tim
On 02/10/2016 04:20 AM, Phan Hồng Phúc wrote:
> Hi Tim,
>
> Could you provide me the full pakage name of annotation type which
> recognize the 'tylenol' name?
> Here are the list of annotation drug type I got, it does not contains
> MedicationMention:
>
> - org.apache.ctakes.drugner.type.ChunkAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.DecimalStrengthAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.DosagesAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.DrugMentionAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.DurationAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.FormAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.FractionStrengthAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.FrequencyAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.FrequencyUnitAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.RangeStrengthAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.RouteAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.StrengthAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.StrengthUnitAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.SubSectionAnnotation [0]
>
>
> - org.apache.ctakes.drugner.type.SuffixStrengthAnnotation [0]
>
> Thank you,
> - Phúc
>
>
> 2016-02-10 2:31 GMT+07:00 Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu>:
>
>> I'm not that familiar with that module but I can confirm that I was able
>> to replicate your output on this example.
>> If it helps at all the MedicationMention type does have a span for the
>> tylenol mention, but obviously doesn't help with all the dosage, route,
>> etc. information you might want.
>> Hopefully one of the devs/maintainers of that module will have some idea.
>> Tim
>>
>>
>> On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
>>> 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
>>>
>>
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
Hi Tim,
Could you provide me the full pakage name of annotation type which
recognize the 'tylenol' name?
Here are the list of annotation drug type I got, it does not contains
MedicationMention:
- org.apache.ctakes.drugner.type.ChunkAnnotation [0]
- org.apache.ctakes.drugner.type.DecimalStrengthAnnotation [0]
- org.apache.ctakes.drugner.type.DosagesAnnotation [0]
- org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation [0]
- org.apache.ctakes.drugner.type.DrugMentionAnnotation [0]
- org.apache.ctakes.drugner.type.DurationAnnotation [0]
- org.apache.ctakes.drugner.type.FormAnnotation [0]
- org.apache.ctakes.drugner.type.FractionStrengthAnnotation [0]
- org.apache.ctakes.drugner.type.FrequencyAnnotation [0]
- org.apache.ctakes.drugner.type.FrequencyUnitAnnotation [0]
- org.apache.ctakes.drugner.type.RangeStrengthAnnotation [0]
- org.apache.ctakes.drugner.type.RouteAnnotation [0]
- org.apache.ctakes.drugner.type.StrengthAnnotation [0]
- org.apache.ctakes.drugner.type.StrengthUnitAnnotation [0]
- org.apache.ctakes.drugner.type.SubSectionAnnotation [0]
- org.apache.ctakes.drugner.type.SuffixStrengthAnnotation [0]
Thank you,
- Phúc
2016-02-10 2:31 GMT+07:00 Miller, Timothy <
Timothy.Miller@childrens.harvard.edu>:
> I'm not that familiar with that module but I can confirm that I was able
> to replicate your output on this example.
> If it helps at all the MedicationMention type does have a span for the
> tylenol mention, but obviously doesn't help with all the dosage, route,
> etc. information you might want.
> Hopefully one of the devs/maintainers of that module will have some idea.
> Tim
>
>
> On 02/09/2016 02:19 PM, Phan HôÌng Phuìc wrote:
> > 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
> >
>
>
Re: Clinical Element Model normalization component
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
I'm not that familiar with that module but I can confirm that I was able
to replicate your output on this example.
If it helps at all the MedicationMention type does have a span for the
tylenol mention, but obviously doesn't help with all the dosage, route,
etc. information you might want.
Hopefully one of the devs/maintainers of that module will have some idea.
Tim
On 02/09/2016 02:19 PM, Phan Hồng Phúc wrote:
> 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
>
Re: Clinical Element Model normalization component
Posted by Phan Hồng Phúc <ph...@gmail.com>.
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