Re: Clinical Processor [EXTERNAL]
Hi Sebastien,
You can refer to this file -
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
for custom dictionary configuration.
On Saturday, August 24, 2019, Sébastien Boussard wrote:
> I am now getting this message as well
>
> On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Sebastien,
> >
> > Can you look at the referenced file
> > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
> >
> > It should be in resources/
> >
> > If it is the default version then it contains the line
> > > value="jdbc:hsqldb:file:resources/org/apache/ctakes/
> dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
> >
> > Can you look at the referenced directory
> > resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> > It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
> >
> > All of the above is for the default configuration.
> >
> > You mentioned
> > >I have the dictionary and I tried to make a custom dictionary.
> >
> > If you made a custom dictionary then you'll need to make the connections
> > appropriately.
> >
> > Sean
> >
> > From: Sébastien Boussard
> > Sent: Friday, August 23, 2019 1:45 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Clinical Processor [EXTERNAL]
> >
> > 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 HH:mm:ss}
> > %5p %c{1} - %m%n].
> >
> > log4j: Adding appender named [consoleAppender] to category [root].
> >
> > 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model
> file:
> > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> >
> > 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> >
> > 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> >
> > 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> >
> > 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> > lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
> >
> > 23 Aug 2019 10:44:06 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
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> > text span: 3
> >
> > 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
> > Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
> >
> > 23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing
> dictionary
> > specifications:
> >
> > 23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-
> 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18&
> s=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> > for user boussard:
> >
> > ..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-
> 2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18&
>
Re: Clinical Processor [EXTERNAL]
I am now getting this message as well
On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> Can you look at the referenced file
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
>
> It should be in resources/
>
> If it is the default version then it contains the line
> value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
>
> Can you look at the referenced directory
> resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ ?
> It should have the files sno_rx_16ab.script and sno_rx_16ab.properties
>
> All of the above is for the default configuration.
>
> You mentioned
> >I have the dictionary and I tried to make a custom dictionary.
>
> If you made a custom dictionary then you'll need to make the connections
> appropriately.
>
> Sean
>
> From: Sébastien Boussard
> Sent: Friday, August 23, 2019 1:45 PM
> To: dev@ctakes.apache.org
> Subject: Re: Clinical Processor [EXTERNAL]
>
> 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 HH:mm:ss}
> %5p %c{1} - %m%n].
>
> log4j: Adding appender named [consoleAppender] to category [root].
>
> 23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
>
> 23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>
> 23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
>
> 23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
>
> 23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>
> 23 Aug 2019 10:44:06 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
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
> text span: 3
>
> 23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
>
> 23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing dictionary
> specifications:
>
> 23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> for user boussard:
>
> ..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LxSE4eAbXm_WMG_Ydxevv4p1bx7iKE2LOQu8G2clC18=YUF4h2Fx488oRBk-V8r1-W1GT1Ol7mTBPlS2AUZqfFU=
> for user boussard has
> been validated
>
>
> 23 Aug 2019 10:44:07 ERROR ProcessLinesClinicalRunner - Initialization of
> annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
> failed. (Descriptor:
> )
>
>
> This is the error message, The last step it completed was looking up the
> umls through the sno_rx16
>
> On Tue, Aug 20, 2019 at 1:26 PM Miller, Timothy <
> timothy.mil...@childrens.harvard.edu> wrote:
>
> > Can you send an error message that is as complete as possible? It is hard
> > to tell from the
Re: Clinical Processor [EXTERNAL]
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 HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
23 Aug 2019 10:44:05 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
23 Aug 2019 10:44:05 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
23 Aug 2019 10:44:05 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
23 Aug 2019 10:44:05 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
23 Aug 2019 10:44:05 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using dictionary
lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
23 Aug 2019 10:44:06 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
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using minimum term
text span: 3
23 Aug 2019 10:44:06 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
23 Aug 2019 10:44:06 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
23 Aug 2019 10:44:06 INFO UmlsUserApprover - Checking UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard:
..23 Aug 2019 10:44:07 INFO UmlsUserApprover - UMLS Account at
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard has
been validated
23 Aug 2019 10:44:07 ERROR ProcessLinesClinicalRunner - Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed. (Descriptor:
)
This is the error message, The last step it completed was looking up the
umls through the sno_rx16
On Tue, Aug 20, 2019 at 1:26 PM Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Can you send an error message that is as complete as possible? It is hard
> to tell from the information you've given.
> Thanks
> Tim
>
>
> -Original Message-
> From: Sébastien Boussard 3d%3fiso-8859-1%3fq%3fs%3de9bastien%3f%3d%20boussard%20%3cbouss...@bu.edu
> %3e>>
> Reply-to:
> To: dev@ctakes.apache.org
> Subject: Clinical Processor [EXTERNAL]
> Date: Thu, 15 Aug 2019 10:28:51 -0700
>
>
> I'm working on making a clinical processor, and I've been having a lot of
> trouble with the JCasTermAnnotator. It's telling me that it's failing to
> initialize. It is connecting to umls and validating. I've had this problem
> for a while, is there any other java class I could use. I have the
> dictionary and I tried to make a custom dictionary.
>
> Thanks,
> Sebastien Boussard
>
>
Re: Relating MeasurementAnnotations to other IdentifiedAnnotations
Thank you Peter and Tim, your responses were very helpful. On Tue, Aug 20, 2019, 5:01 PM Peter Abramowitsch wrote: > Hi Jeff > > I've experimented with three approaches. > > One is with the LabValueFinder which is included in the cTakes release - > that looks specifically for values associated with LabMentions. It also > has an "eager" mode where it converts some MedicationMentions into > LabMentions, when the context seems right. O2, Sodium etc. I can't say > it works all that well and it is not capable of many different semantic > forms of the Name/Value association. It is also too eager.. sometimes > creating LabMentions out of Medications when it shouldn't. > > Another approach was to use something like Stanford's TokensRegex, that > allows you to construct regex-like rules where the segments are not strings > but Tokens, where you can query the attributes like POS, and NER . For > Ctakes I had to adapt a UIMA package that must have been someone's thesis > project from the university of Nantes. > > Copyright 2015 - CNRS (Centre National de Recherche Scientifique) > package fr.univnantes.lina.uima.tkregex > > What I have is not ready for prime time and is still very rough. It works > well but only for a limited set of rules > > I used it to create a vitals detector. Here's a snippet of the rules that > this package loads in at runtime, that creates an annotation called WGT > given these matchers > matcher NUM: [ postag == "CD" ]; > matcher BE: [ lemma == "be" | lemma == "at"]; > matcher WT: /(?i)^wt|^weight/; > matcher WUOM: /(?i)^kg|^lb|^pounds/; > term "WGT": WT BE? SYM? NUM WUOM; > > The last approach was a home-built mechanism using the ConllDependencyNode > collection and the RelationArguments to detect the same connection between > certain typed pairs of Identified annotations. > > Problem is. I've always been in prototyping mode and never had time to push > these methods to production ready status > > Peter > > On Tue, Aug 20, 2019 at 1:15 PM Jeffrey Miller wrote: > > > Hi, > > > > Is there any configuration or component in cTAKES that can be used to > > attribute a measurement annotation to another annotation that it applies > > to? For example, for "2 mm incision" where we relate "2 mm" to > "incision"? > > It looks like there might be a roundabout way to find the head of the > span > > of the MeasurementAnnotation in the output of the dependency parser, but > I > > was wondering if this has been explored before? Perhaps the > > RelationExtractor component? > > > > I also have another more general question if anyone can help- how does > the > > structure of the cTAKES type system effect how cTAKES works? I am looking > > for a general intuition of how the structure of the typesystem drives the > > larger cTAKES architecture? > > > > Thanks! > > Jeff > > >
