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Posted to user@ctakes.apache.org by Sajit Kumar <ku...@gmail.com> on 2019/02/03 14:31:14 UTC
New to cTakes and need help
Hi All,
I am new to cTakes. I have heard great things about cTakes in processing
clinical notes. I have been able to successfully install and launch cTakes
applications. However, I have not been able to find enough documentation
for the XMI output from these applications such as CPE etc. If anyone can
guide me to some documentation to understand the structure of these outputs
that would be helpful.
Additionally, I am working on a task where i am interested in extracting
the UMLS, SNOMED medical concepts from the clinical notes. However, i see
that the output usually has lot of information that is not relevant to my
task. I tried my hands at creating a custom pipeline to get rid of this
information. But it was throwing an exception. Please find below the
script.
// *** Piper File ***
// Created by Sajit
// on February 03, 2019
// Text Files Reader
// Reads document texts from text files specified in a provided list.
# files The text files to be loaded
reader org.apache.ctakes.core.cr.TextReader
files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt
// UMLS Dictionary Lookup (Old)
// Annotates clinically-relevant terms. This is an older, slower
dictionary lookup implementation.
add org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
// XMI Writer
// Writes XMI files with full representation of input text and all
extracted information.
# OutputDirectory Output directory to write xmi files
add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
This passes the validation but fails to execute.
Please tell me if my approach is right or wrong. And is it possible to trim
the XMI outputs based on ones need in the cTakes tool.
Any suggestion or help is most welcome. Thanks.
Regards,
Sajit
Re: New to cTakes and need help
Posted by gandhi rajan <ga...@gmail.com>.
Sorry Sajit. I don't have enough expertise to help you out on this. You may
need to check out ctakes component user guide to see if it helps or look at
the code.
Sean and Tim, any thoughts?
On Tuesday, February 5, 2019, Sajit Kumar <ku...@gmail.com> wrote:
> Hi Gandhi,
>
> Thanks for the reply. Can you please help me with some documentation on
> the XML file structure or point me to some documentation. That would be
> of great help.
>
> Regards,
> Sajit
>
> On Mon, Feb 4, 2019 at 8:40 PM gandhi rajan <ga...@gmail.com>
> wrote:
>
>> Hi Sajit, I m not sure whether creating custom piper is gonna help as I
>> believe default clinical pipeline has the bare minimum but necessary stuff.
>>
>> You can probably parse the XML and extract out the stuff you want.
>>
>> On Monday, February 4, 2019, Sajit Kumar <ku...@gmail.com>
>> wrote:
>>
>>> Hi Gandhi,
>>>
>>> Thanks for your reply.
>>>
>>> Let me elaborate my task. I need to extract the CUIs for the medical
>>> concepts in clinical notes. I believe cTakes can be a very good tool for
>>> this.
>>> I went through the default clinical pipeline. The pipeline is has
>>> various tasks in the pipe such as boundary detection, tokenization, entity
>>> recognition etc. I believe the output XMI document also has sections for
>>> each of these tasks. However, as I am only interested in the CUIs for
>>> medical concepts. I would only be interested in entity recognition and
>>> entity properties in my output. Is it possible to create a custom pipeline
>>> based on this. Or is it possible to turn off the output of unwanted
>>> sections. I hope you understand what I am trying to say. Please advise.
>>>
>>> Also is there any documentation on the structure of cTAKES output files
>>> such as XMI files.
>>>
>>> Looking forward to your response.
>>>
>>> Regards,
>>> Sajit
>>>
>>> On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhirajan.n@gmail.com wrote:
>>>
>>>> Hi Sajit, I would say default clinical pipeline is the best place to
>>>> start for a beginner - https://cwiki.apache.org/
>>>> confluence/display/CTAKES/Default+Clinical+Pipeline
>>>>
>>>> Also you got to elaborate what information you are looking for when you
>>>> say many of the information are irrelevant for you.
>>>>
>>>> On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi All,
>>>>>
>>>>> I am new to cTakes. I have heard great things about cTakes in
>>>>> processing clinical notes. I have been able to successfully install and
>>>>> launch cTakes applications. However, I have not been able to find enough
>>>>> documentation for the XMI output from these applications such as CPE etc.
>>>>> If anyone can guide me to some documentation to understand the structure of
>>>>> these outputs that would be helpful.
>>>>>
>>>>> Additionally, I am working on a task where i am interested in
>>>>> extracting the UMLS, SNOMED medical concepts from the clinical notes.
>>>>> However, i see that the output usually has lot of information that is not
>>>>> relevant to my task. I tried my hands at creating a custom pipeline to get
>>>>> rid of this information. But it was throwing an exception. Please find
>>>>> below the script.
>>>>>
>>>>> // *** Piper File ***
>>>>> // Created by Sajit
>>>>> // on February 03, 2019
>>>>>
>>>>>
>>>>> // Text Files Reader
>>>>> // Reads document texts from text files specified in a provided list.
>>>>> # files The text files to be loaded
>>>>> reader org.apache.ctakes.core.cr.TextReader
>>>>> files=C:\apache-ctakes-4.0.0\testdata\Input\
>>>>> SampleInputRadiologyNotes.txt
>>>>>
>>>>> // UMLS Dictionary Lookup (Old)
>>>>> // Annotates clinically-relevant terms. This is an older, slower
>>>>> dictionary lookup implementation.
>>>>> add org.apache.ctakes.dictionary.lookup.ae.
>>>>> UmlsDictionaryLookupAnnotator
>>>>>
>>>>> // XMI Writer
>>>>> // Writes XMI files with full representation of input text and all
>>>>> extracted information.
>>>>> # OutputDirectory Output directory to write xmi files
>>>>> add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
>>>>> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>>>>>
>>>>> This passes the validation but fails to execute.
>>>>> Please tell me if my approach is right or wrong. And is it possible to
>>>>> trim the XMI outputs based on ones need in the cTakes tool.
>>>>>
>>>>> Any suggestion or help is most welcome. Thanks.
>>>>>
>>>>> Regards,
>>>>> Sajit
>>>>>
>>>>
>>>>
>>>> --
>>>> Regards,
>>>> Gandhi
>>>>
>>>> "The best way to find urself is to lose urself in the service of others
>>>> !!!"
>>>>
>>>>
>>
>> --
>> Regards,
>> Gandhi
>>
>> "The best way to find urself is to lose urself in the service of others
>> !!!"
>>
>>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: New to cTakes and need help
Posted by Sajit Kumar <ku...@gmail.com>.
Hi Gandhi,
Thanks for the reply. Can you please help me with some documentation on the
XML file structure or point me to some documentation. That would be
of great help.
Regards,
Sajit
On Mon, Feb 4, 2019 at 8:40 PM gandhi rajan <ga...@gmail.com> wrote:
> Hi Sajit, I m not sure whether creating custom piper is gonna help as I
> believe default clinical pipeline has the bare minimum but necessary stuff.
>
> You can probably parse the XML and extract out the stuff you want.
>
> On Monday, February 4, 2019, Sajit Kumar <ku...@gmail.com> wrote:
>
>> Hi Gandhi,
>>
>> Thanks for your reply.
>>
>> Let me elaborate my task. I need to extract the CUIs for the medical
>> concepts in clinical notes. I believe cTakes can be a very good tool for
>> this.
>> I went through the default clinical pipeline. The pipeline is has various
>> tasks in the pipe such as boundary detection, tokenization, entity
>> recognition etc. I believe the output XMI document also has sections for
>> each of these tasks. However, as I am only interested in the CUIs for
>> medical concepts. I would only be interested in entity recognition and
>> entity properties in my output. Is it possible to create a custom pipeline
>> based on this. Or is it possible to turn off the output of unwanted
>> sections. I hope you understand what I am trying to say. Please advise.
>>
>> Also is there any documentation on the structure of cTAKES output files
>> such as XMI files.
>>
>> Looking forward to your response.
>>
>> Regards,
>> Sajit
>>
>> On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhirajan.n@gmail.com wrote:
>>
>>> Hi Sajit, I would say default clinical pipeline is the best place to
>>> start for a beginner -
>>> https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
>>>
>>> Also you got to elaborate what information you are looking for when you
>>> say many of the information are irrelevant for you.
>>>
>>> On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I am new to cTakes. I have heard great things about cTakes in
>>>> processing clinical notes. I have been able to successfully install and
>>>> launch cTakes applications. However, I have not been able to find enough
>>>> documentation for the XMI output from these applications such as CPE etc.
>>>> If anyone can guide me to some documentation to understand the structure of
>>>> these outputs that would be helpful.
>>>>
>>>> Additionally, I am working on a task where i am interested in
>>>> extracting the UMLS, SNOMED medical concepts from the clinical notes.
>>>> However, i see that the output usually has lot of information that is not
>>>> relevant to my task. I tried my hands at creating a custom pipeline to get
>>>> rid of this information. But it was throwing an exception. Please find
>>>> below the script.
>>>>
>>>> // *** Piper File ***
>>>> // Created by Sajit
>>>> // on February 03, 2019
>>>>
>>>>
>>>> // Text Files Reader
>>>> // Reads document texts from text files specified in a provided list.
>>>> # files The text files to be loaded
>>>> reader org.apache.ctakes.core.cr.TextReader
>>>> files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt
>>>>
>>>> // UMLS Dictionary Lookup (Old)
>>>> // Annotates clinically-relevant terms. This is an older, slower
>>>> dictionary lookup implementation.
>>>> add org.apache.ctakes.dictionary.lookup.ae
>>>> .UmlsDictionaryLookupAnnotator
>>>>
>>>> // XMI Writer
>>>> // Writes XMI files with full representation of input text and all
>>>> extracted information.
>>>> # OutputDirectory Output directory to write xmi files
>>>> add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
>>>> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>>>>
>>>> This passes the validation but fails to execute.
>>>> Please tell me if my approach is right or wrong. And is it possible to
>>>> trim the XMI outputs based on ones need in the cTakes tool.
>>>>
>>>> Any suggestion or help is most welcome. Thanks.
>>>>
>>>> Regards,
>>>> Sajit
>>>>
>>>
>>>
>>> --
>>> Regards,
>>> Gandhi
>>>
>>> "The best way to find urself is to lose urself in the service of others
>>> !!!"
>>>
>>>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
>
Re: New to cTakes and need help [EXTERNAL]
Posted by Greg Silverman <gm...@umn.edu>.
I've extracted data from XMI using python. It gets a little ugly, but it
gives you an appreciation for the structure.
On Mon, Feb 4, 2019 at 9:17 AM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> Or you can get types within UIMA using UIMAfit class called
> org.apache.uima.fit.util.JCasUtil. This class shows an example of using it
> to get cuis:
>
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java?view=markup
> which references this class as well:
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java?view=markup
>
> My normal workflow is to open the xmi files in the CVD to understand the
> structure of the CAS, and then you can write code using JCasUtil to extract
> pieces of information from the CAS without having to parse the xml
> manually. The above 2 classes show you one example of how that might work.
>
> Tim
>
>
> -----Original Message-----
> *From*: gandhi rajan <gandhirajan.n@gmail.com
> <gandhi%20rajan%20%3cgandhirajan.n@gmail.com%3e>>
> Reply-to: <us...@ctakes.apache.org>
> *To*: user@ctakes.apache.org <user@ctakes.apache.org
> <%22user@ctakes.apache.org%22%20%3cuser@ctakes.apache.org%3e>>
> *Subject*: Re: New to cTakes and need help [EXTERNAL]
> *Date*: Mon, 4 Feb 2019 20:40:30 +0530
>
> Hi Sajit, I m not sure whether creating custom piper is gonna help as I
> believe default clinical pipeline has the bare minimum but necessary stuff.
>
> You can probably parse the XML and extract out the stuff you want.
>
> On Monday, February 4, 2019, Sajit Kumar <ku...@gmail.com> wrote:
>
> Hi Gandhi,
>
> Thanks for your reply.
>
> Let me elaborate my task. I need to extract the CUIs for the medical
> concepts in clinical notes. I believe cTakes can be a very good tool for
> this.
> I went through the default clinical pipeline. The pipeline is has various
> tasks in the pipe such as boundary detection, tokenization, entity
> recognition etc. I believe the output XMI document also has sections for
> each of these tasks. However, as I am only interested in the CUIs for
> medical concepts. I would only be interested in entity recognition and
> entity properties in my output. Is it possible to create a custom pipeline
> based on this. Or is it possible to turn off the output of unwanted
> sections. I hope you understand what I am trying to say. Please advise.
>
> Also is there any documentation on the structure of cTAKES output files
> such as XMI files.
>
> Looking forward to your response.
>
> Regards,
> Sajit
>
> On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhirajan.n@gmail.com wrote:
>
> Hi Sajit, I would say default clinical pipeline is the best place to start
> for a beginner -
> https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Default-2BClinical-2BPipeline&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=vgITkX94MJWHn_ZcTDGOIF1unvHBy4hsozSAQDNxVPc&e=>
>
> Also you got to elaborate what information you are looking for when you
> say many of the information are irrelevant for you.
>
> On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com> wrote:
>
> Hi All,
>
> I am new to cTakes. I have heard great things about cTakes in processing
> clinical notes. I have been able to successfully install and launch cTakes
> applications. However, I have not been able to find enough documentation
> for the XMI output from these applications such as CPE etc. If anyone can
> guide me to some documentation to understand the structure of these outputs
> that would be helpful.
>
> Additionally, I am working on a task where i am interested in extracting
> the UMLS, SNOMED medical concepts from the clinical notes. However, i see
> that the output usually has lot of information that is not relevant to my
> task. I tried my hands at creating a custom pipeline to get rid of this
> information. But it was throwing an exception. Please find below the
> script.
>
> // *** Piper File ***
> // Created by Sajit
> // on February 03, 2019
>
>
> // Text Files Reader
> // Reads document texts from text files specified in a provided list.
> # files The text files to be loaded
> reader org.apache.ctakes.core.cr
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.core.cr&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=L-lJTun5qSIwX1uKN80rjeWGdgyJHcSmgsPW9KCrZqw&e=>.TextReader
> files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt
>
> // UMLS Dictionary Lookup (Old)
> // Annotates clinically-relevant terms. This is an older, slower
> dictionary lookup implementation.
> add org.apache.ctakes.dictionary.lookup.ae
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=EDNf4iv0l1yNCYVQY60x7dBnic7yrCIOAJaqLKbG62k&e=>
> .UmlsDictionaryLookupAnnotator
>
> // XMI Writer
> // Writes XMI files with full representation of input text and all
> extracted information.
> # OutputDirectory Output directory to write xmi files
> add org.apache.ctakes.core.cc
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.core.cc&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=AOpVB1o8HgyIvrpNjByVtDgVmNTIqX-IPIPnQDu2Ns0&e=>.XmiWriterCasConsumerCtakes
> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>
> This passes the validation but fails to execute.
> Please tell me if my approach is right or wrong. And is it possible to
> trim the XMI outputs based on ones need in the cTakes tool.
>
> Any suggestion or help is most welcome. Thanks.
>
> Regards,
> Sajit
>
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
>
>
>
>
>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Cardiovascular Informatics <http://www.med.umn.edu/cardiology/>
University of Minnesota
gms@umn.edu
› evaluate-it.org ‹
Re: New to cTakes and need help [EXTERNAL]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Or you can get types within UIMA using UIMAfit class called org.apache.uima.fit.util.JCasUtil. This class shows an example of using it to get cuis:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java?view=markup
which references this class as well:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java?view=markup
My normal workflow is to open the xmi files in the CVD to understand the structure of the CAS, and then you can write code using JCasUtil to extract pieces of information from the CAS without having to parse the xml manually. The above 2 classes show you one example of how that might work.
Tim
-----Original Message-----
From: gandhi rajan <gandhirajan.n@gmail.com<mailto:gandhi%20rajan%20%3cgandhirajan.n@gmail.com%3e>>
Reply-to: <us...@ctakes.apache.org>
To: user@ctakes.apache.org <user@ctakes.apache.org<mailto:%22user@ctakes.apache.org%22%20%3cuser@ctakes.apache.org%3e>>
Subject: Re: New to cTakes and need help [EXTERNAL]
Date: Mon, 4 Feb 2019 20:40:30 +0530
Hi Sajit, I m not sure whether creating custom piper is gonna help as I believe default clinical pipeline has the bare minimum but necessary stuff.
You can probably parse the XML and extract out the stuff you want.
On Monday, February 4, 2019, Sajit Kumar <ku...@gmail.com>> wrote:
Hi Gandhi,
Thanks for your reply.
Let me elaborate my task. I need to extract the CUIs for the medical concepts in clinical notes. I believe cTakes can be a very good tool for this.
I went through the default clinical pipeline. The pipeline is has various tasks in the pipe such as boundary detection, tokenization, entity recognition etc. I believe the output XMI document also has sections for each of these tasks. However, as I am only interested in the CUIs for medical concepts. I would only be interested in entity recognition and entity properties in my output. Is it possible to create a custom pipeline based on this. Or is it possible to turn off the output of unwanted sections. I hope you understand what I am trying to say. Please advise.
Also is there any documentation on the structure of cTAKES output files such as XMI files.
Looking forward to your response.
Regards,
Sajit
On Sun, 3 Feb, 2019, 20:48 gandhi rajan <ga...@gmail.com> wrote:
Hi Sajit, I would say default clinical pipeline is the best place to start for a beginner - https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline<https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Default-2BClinical-2BPipeline&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=vgITkX94MJWHn_ZcTDGOIF1unvHBy4hsozSAQDNxVPc&e=>
Also you got to elaborate what information you are looking for when you say many of the information are irrelevant for you.
On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com>> wrote:
Hi All,
I am new to cTakes. I have heard great things about cTakes in processing clinical notes. I have been able to successfully install and launch cTakes applications. However, I have not been able to find enough documentation for the XMI output from these applications such as CPE etc. If anyone can guide me to some documentation to understand the structure of these outputs that would be helpful.
Additionally, I am working on a task where i am interested in extracting the UMLS, SNOMED medical concepts from the clinical notes. However, i see that the output usually has lot of information that is not relevant to my task. I tried my hands at creating a custom pipeline to get rid of this information. But it was throwing an exception. Please find below the script.
// *** Piper File ***
// Created by Sajit
// on February 03, 2019
// Text Files Reader
// Reads document texts from text files specified in a provided list.
# files The text files to be loaded
reader org.apache.ctakes.core.cr<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.core.cr&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=L-lJTun5qSIwX1uKN80rjeWGdgyJHcSmgsPW9KCrZqw&e=>.TextReader files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt
// UMLS Dictionary Lookup (Old)
// Annotates clinically-relevant terms. This is an older, slower dictionary lookup implementation.
add org.apache.ctakes.dictionary.lookup.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__lookup.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=EDNf4iv0l1yNCYVQY60x7dBnic7yrCIOAJaqLKbG62k&e=>.UmlsDictionaryLookupAnnotator
// XMI Writer
// Writes XMI files with full representation of input text and all extracted information.
# OutputDirectory Output directory to write xmi files
add org.apache.ctakes.core.cc<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.core.cc&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ysAxxHm1TU8AhZe18e19G1np5RXR9H2kgXRrY9jLHMI&s=AOpVB1o8HgyIvrpNjByVtDgVmNTIqX-IPIPnQDu2Ns0&e=>.XmiWriterCasConsumerCtakes OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
This passes the validation but fails to execute.
Please tell me if my approach is right or wrong. And is it possible to trim the XMI outputs based on ones need in the cTakes tool.
Any suggestion or help is most welcome. Thanks.
Regards,
Sajit
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: New to cTakes and need help
Posted by gandhi rajan <ga...@gmail.com>.
Hi Sajit, I m not sure whether creating custom piper is gonna help as I
believe default clinical pipeline has the bare minimum but necessary stuff.
You can probably parse the XML and extract out the stuff you want.
On Monday, February 4, 2019, Sajit Kumar <ku...@gmail.com> wrote:
> Hi Gandhi,
>
> Thanks for your reply.
>
> Let me elaborate my task. I need to extract the CUIs for the medical
> concepts in clinical notes. I believe cTakes can be a very good tool for
> this.
> I went through the default clinical pipeline. The pipeline is has various
> tasks in the pipe such as boundary detection, tokenization, entity
> recognition etc. I believe the output XMI document also has sections for
> each of these tasks. However, as I am only interested in the CUIs for
> medical concepts. I would only be interested in entity recognition and
> entity properties in my output. Is it possible to create a custom pipeline
> based on this. Or is it possible to turn off the output of unwanted
> sections. I hope you understand what I am trying to say. Please advise.
>
> Also is there any documentation on the structure of cTAKES output files
> such as XMI files.
>
> Looking forward to your response.
>
> Regards,
> Sajit
>
> On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhirajan.n@gmail.com wrote:
>
>> Hi Sajit, I would say default clinical pipeline is the best place to
>> start for a beginner - https://cwiki.apache.org/
>> confluence/display/CTAKES/Default+Clinical+Pipeline
>>
>> Also you got to elaborate what information you are looking for when you
>> say many of the information are irrelevant for you.
>>
>> On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com>
>> wrote:
>>
>>> Hi All,
>>>
>>> I am new to cTakes. I have heard great things about cTakes in processing
>>> clinical notes. I have been able to successfully install and launch cTakes
>>> applications. However, I have not been able to find enough documentation
>>> for the XMI output from these applications such as CPE etc. If anyone can
>>> guide me to some documentation to understand the structure of these outputs
>>> that would be helpful.
>>>
>>> Additionally, I am working on a task where i am interested in extracting
>>> the UMLS, SNOMED medical concepts from the clinical notes. However, i see
>>> that the output usually has lot of information that is not relevant to my
>>> task. I tried my hands at creating a custom pipeline to get rid of this
>>> information. But it was throwing an exception. Please find below the
>>> script.
>>>
>>> // *** Piper File ***
>>> // Created by Sajit
>>> // on February 03, 2019
>>>
>>>
>>> // Text Files Reader
>>> // Reads document texts from text files specified in a provided list.
>>> # files The text files to be loaded
>>> reader org.apache.ctakes.core.cr.TextReader
>>> files=C:\apache-ctakes-4.0.0\testdata\Input\
>>> SampleInputRadiologyNotes.txt
>>>
>>> // UMLS Dictionary Lookup (Old)
>>> // Annotates clinically-relevant terms. This is an older, slower
>>> dictionary lookup implementation.
>>> add org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
>>>
>>> // XMI Writer
>>> // Writes XMI files with full representation of input text and all
>>> extracted information.
>>> # OutputDirectory Output directory to write xmi files
>>> add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
>>> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>>>
>>> This passes the validation but fails to execute.
>>> Please tell me if my approach is right or wrong. And is it possible to
>>> trim the XMI outputs based on ones need in the cTakes tool.
>>>
>>> Any suggestion or help is most welcome. Thanks.
>>>
>>> Regards,
>>> Sajit
>>>
>>
>>
>> --
>> Regards,
>> Gandhi
>>
>> "The best way to find urself is to lose urself in the service of others
>> !!!"
>>
>>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: New to cTakes and need help
Posted by Sajit Kumar <ku...@gmail.com>.
Hi Gandhi,
Thanks for your reply.
Let me elaborate my task. I need to extract the CUIs for the medical
concepts in clinical notes. I believe cTakes can be a very good tool for
this.
I went through the default clinical pipeline. The pipeline is has various
tasks in the pipe such as boundary detection, tokenization, entity
recognition etc. I believe the output XMI document also has sections for
each of these tasks. However, as I am only interested in the CUIs for
medical concepts. I would only be interested in entity recognition and
entity properties in my output. Is it possible to create a custom pipeline
based on this. Or is it possible to turn off the output of unwanted
sections. I hope you understand what I am trying to say. Please advise.
Also is there any documentation on the structure of cTAKES output files
such as XMI files.
Looking forward to your response.
Regards,
Sajit
On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhirajan.n@gmail.com wrote:
> Hi Sajit, I would say default clinical pipeline is the best place to start
> for a beginner -
> https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
>
> Also you got to elaborate what information you are looking for when you
> say many of the information are irrelevant for you.
>
> On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com> wrote:
>
>> Hi All,
>>
>> I am new to cTakes. I have heard great things about cTakes in processing
>> clinical notes. I have been able to successfully install and launch cTakes
>> applications. However, I have not been able to find enough documentation
>> for the XMI output from these applications such as CPE etc. If anyone can
>> guide me to some documentation to understand the structure of these outputs
>> that would be helpful.
>>
>> Additionally, I am working on a task where i am interested in extracting
>> the UMLS, SNOMED medical concepts from the clinical notes. However, i see
>> that the output usually has lot of information that is not relevant to my
>> task. I tried my hands at creating a custom pipeline to get rid of this
>> information. But it was throwing an exception. Please find below the
>> script.
>>
>> // *** Piper File ***
>> // Created by Sajit
>> // on February 03, 2019
>>
>>
>> // Text Files Reader
>> // Reads document texts from text files specified in a provided list.
>> # files The text files to be loaded
>> reader org.apache.ctakes.core.cr.TextReader
>> files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt
>>
>> // UMLS Dictionary Lookup (Old)
>> // Annotates clinically-relevant terms. This is an older, slower
>> dictionary lookup implementation.
>> add org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
>>
>> // XMI Writer
>> // Writes XMI files with full representation of input text and all
>> extracted information.
>> # OutputDirectory Output directory to write xmi files
>> add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
>> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>>
>> This passes the validation but fails to execute.
>> Please tell me if my approach is right or wrong. And is it possible to
>> trim the XMI outputs based on ones need in the cTakes tool.
>>
>> Any suggestion or help is most welcome. Thanks.
>>
>> Regards,
>> Sajit
>>
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
>
Re: New to cTakes and need help
Posted by gandhi rajan <ga...@gmail.com>.
Hi Sajit, I would say default clinical pipeline is the best place to start
for a beginner -
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
Also you got to elaborate what information you are looking for when you say
many of the information are irrelevant for you.
On Sunday, February 3, 2019, Sajit Kumar <ku...@gmail.com> wrote:
> Hi All,
>
> I am new to cTakes. I have heard great things about cTakes in processing
> clinical notes. I have been able to successfully install and launch cTakes
> applications. However, I have not been able to find enough documentation
> for the XMI output from these applications such as CPE etc. If anyone can
> guide me to some documentation to understand the structure of these outputs
> that would be helpful.
>
> Additionally, I am working on a task where i am interested in extracting
> the UMLS, SNOMED medical concepts from the clinical notes. However, i see
> that the output usually has lot of information that is not relevant to my
> task. I tried my hands at creating a custom pipeline to get rid of this
> information. But it was throwing an exception. Please find below the
> script.
>
> // *** Piper File ***
> // Created by Sajit
> // on February 03, 2019
>
>
> // Text Files Reader
> // Reads document texts from text files specified in a provided list.
> # files The text files to be loaded
> reader org.apache.ctakes.core.cr.TextReader files=C:\apache-ctakes-4.0.0\
> testdata\Input\SampleInputRadiologyNotes.txt
>
> // UMLS Dictionary Lookup (Old)
> // Annotates clinically-relevant terms. This is an older, slower
> dictionary lookup implementation.
> add org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
>
> // XMI Writer
> // Writes XMI files with full representation of input text and all
> extracted information.
> # OutputDirectory Output directory to write xmi files
> add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
> OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output
>
> This passes the validation but fails to execute.
> Please tell me if my approach is right or wrong. And is it possible to
> trim the XMI outputs based on ones need in the cTakes tool.
>
> Any suggestion or help is most welcome. Thanks.
>
> Regards,
> Sajit
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"