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Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2017/03/06 17:08:01 UTC
Re: [Relation_Extraction] Ctakes relation extraction
Hi Oleg,
Currently, cTAKES only includes the models for locationOf and DegreeOf relations. Even though I added the code for other relation types a while ago, we haven’t released the models (mostly because the performance on those relation types are not satisfactory).
So, you should just ignore everything except locationOf and degreeOf relations.
Hope this helps,
Dima
> On Mar 6, 2017, at 03:28, Oleg Bogatiryov <ol...@ctco.lv> wrote:
>
> Hi Dmitriy.
>
> Thank you for your response.
>
> I am using RelationExtractorPipeline class to generate xmi's.
> I got good results for LocationOfRelationExtractorAnnotator and
> DegreeOfRelationExtratorAnnotator.
>
> I've edited RelationExtractorAggregate.xml file with adding more annotators.
> There are some results but category is displayed like "O".
>
> For example working results:
>
> class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> Category: location_of
> Argument1: blood pressure
> Role: Argument
> Argument2: blood
> Role: Related_to
>
>
> class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
> Category: degree_of
> Argument1: anxiety
> Role: Argument
> Argument2: acute
> Role: Related_to
>
>
>
> And non-properly working
>
> class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
> Category: O
> Argument1: anxiety
> Role: Argument
> Argument2: anxiety
> Role: Related_to
>
> class
> org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
> Category: O
> Argument1: anxiety
> Role: Argument
> Argument2: symptoms
> Role: Related_to
>
> Category is O.
> Could you please help me with getting right results for other relations
> extraction annotators ?
>
> I've attached my ae descriptors. They are primitive and included into
> RelationExtractionAggregate.xml.
> Please remove .ze from the achive and uzip it.
>
> Thanks in advance,
> Oleg.
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Tuesday, February 28, 2017 1:58
> To: dev@ctakes.apache.org
> Subject: Re: Ctakes relation extraction
>
> Hi Oleg,
>
> You may want to look into learning about UIMA and UIMAFIT.
>
> Once you are somewhat comfortable with these frameworks, take a look at the
> package:
>
> ctakes/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/
>
> There are several pipelines that may work for you (e.g. take a look at
> RelationExtractorPipeline.java). Many of them should generate XMI files
> which contain the relation annotations you are looking for. Once you have
> generated the XMI files, you can parse them using UIMAFIT. E.g. take a look
> at RelationAnnotationViewer.java which you should use as an example.
>
> Hope this helps!
>
> Dima
>
>
>
>> On Feb 24, 2017, at 03:07, Oleg Bogatiryov <ol...@ctco.lv>
>> wrote:
>>
>> Hi Dmitriy.
>>
>> Thank you for your reply.
>>
>> I am not sure how can I extract location_of and degree_of.
>> AggregateTemplateFiller doesn't return anything in CVD as well as
>> TemporalAggregatePipeline.
>> There is BinaryTextRelation class that as I understand should fill in
>> relations but no data is displayed.
>>
>> I was trying to execute RelationExtractorPipelineSingleCas but it
>> doesn't print anything related to relations.
>>
>> Could you please help me with extraction of relations from the med text ?
>>
>> As I am a new to ctakes and uima could you please provide step to step
>> instructions and exact classes to use.
>>
>>
>> Thanks in advance,
>> Oleg.
>>
>> -----Original Message-----
>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> Sent: 20 февраля 2017 г. 17:48
>> To: dev@ctakes.apache.org
>> Subject: Re: Ctakes relation extraction
>>
>> Hi Oleg,
>>
>> The relation extraction AE currently only handles location_of and
>> degree_of relations as described here:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/
>>
>> The dependencies are handled by the dependency parser (i.e. a separate
>> module).
>>
>> So you’ll need to run both and collect all annotated relations from
>> the the CAS.
>>
>> Hope this helps.
>>
>> Dima
>>
>>
>>
>>> On Feb 20, 2017, at 01:31, Oleg Bogatiryov <ol...@ctco.lv>
>>> wrote:
>>>
>>> Hello to everyone.
>>>
>>>
>>>
>>> I am pleased to join the group.
>>>
>>>
>>>
>>> I am trying to extract relation from the document.
>>>
>>> Ideally I'd like to get the graph or tree of dependencies/relations
>>> from the clinical documents.
>>>
>>>
>>>
>>> Could you please let me know how can I achieve it ?
>>>
>>>
>>>
>>> I am able to run CVD and RelationExtractorAggregate analysis engine
>>> but there is no useful information
>>>
>>> in results that can be used in order to build a relation graph.
>>>
>>>
>>>
>>> Thanks in advance,
>>>
>>> Oleg.
>>>
>>
>
> <analysis_engine.zip.ze>
Re: [Relation_Extraction] Ctakes relation extraction
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi Oleg,
Sorry, unfortunately there is no clarity on that. We are in the process of applying for funding to make that happen.
Dima
> On Mar 7, 2017, at 01:30, Oleg Bogatiryov <ol...@ctco.lv> wrote:
>
> Hi Dmitriy.
>
> Thank you for your response.
>
> Could you please let me know when the other types of relations will be released ?
> Release number or date if possible please.
>
> Thanks in advance.
>
> ----- Original Message -----
> From: "ddligach" <dd...@luc.edu>
> To: "Oleg Bogatiryov" <ol...@ctco.lv>
> Cc: dev@ctakes.apache.org
> Sent: Monday, March 6, 2017 8:08:01 PM
> Subject: Re: [Relation_Extraction] Ctakes relation extraction
>
> Hi Oleg,
>
> Currently, cTAKES only includes the models for locationOf and DegreeOf relations. Even though I added the code for other relation types a while ago, we haven’t released the models (mostly because the performance on those relation types are not satisfactory).
>
> So, you should just ignore everything except locationOf and degreeOf relations.
>
> Hope this helps,
>
> Dima
>
>
>
>> On Mar 6, 2017, at 03:28, Oleg Bogatiryov <ol...@ctco.lv> wrote:
>>
>> Hi Dmitriy.
>>
>> Thank you for your response.
>>
>> I am using RelationExtractorPipeline class to generate xmi's.
>> I got good results for LocationOfRelationExtractorAnnotator and
>> DegreeOfRelationExtratorAnnotator.
>>
>> I've edited RelationExtractorAggregate.xml file with adding more annotators.
>> There are some results but category is displayed like "O".
>>
>> For example working results:
>>
>> class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
>> Category: location_of
>> Argument1: blood pressure
>> Role: Argument
>> Argument2: blood
>> Role: Related_to
>>
>>
>> class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
>> Category: degree_of
>> Argument1: anxiety
>> Role: Argument
>> Argument2: acute
>> Role: Related_to
>>
>>
>>
>> And non-properly working
>>
>> class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
>> Category: O
>> Argument1: anxiety
>> Role: Argument
>> Argument2: anxiety
>> Role: Related_to
>>
>> class
>> org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
>> Category: O
>> Argument1: anxiety
>> Role: Argument
>> Argument2: symptoms
>> Role: Related_to
>>
>> Category is O.
>> Could you please help me with getting right results for other relations
>> extraction annotators ?
>>
>> I've attached my ae descriptors. They are primitive and included into
>> RelationExtractionAggregate.xml.
>> Please remove .ze from the achive and uzip it.
>>
>> Thanks in advance,
>> Oleg.
>>
>>
>> -----Original Message-----
>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> Sent: Tuesday, February 28, 2017 1:58
>> To: dev@ctakes.apache.org
>> Subject: Re: Ctakes relation extraction
>>
>> Hi Oleg,
>>
>> You may want to look into learning about UIMA and UIMAFIT.
>>
>> Once you are somewhat comfortable with these frameworks, take a look at the
>> package:
>>
>> ctakes/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/
>>
>> There are several pipelines that may work for you (e.g. take a look at
>> RelationExtractorPipeline.java). Many of them should generate XMI files
>> which contain the relation annotations you are looking for. Once you have
>> generated the XMI files, you can parse them using UIMAFIT. E.g. take a look
>> at RelationAnnotationViewer.java which you should use as an example.
>>
>> Hope this helps!
>>
>> Dima
>>
>>
>>
>>> On Feb 24, 2017, at 03:07, Oleg Bogatiryov <ol...@ctco.lv>
>>> wrote:
>>>
>>> Hi Dmitriy.
>>>
>>> Thank you for your reply.
>>>
>>> I am not sure how can I extract location_of and degree_of.
>>> AggregateTemplateFiller doesn't return anything in CVD as well as
>>> TemporalAggregatePipeline.
>>> There is BinaryTextRelation class that as I understand should fill in
>>> relations but no data is displayed.
>>>
>>> I was trying to execute RelationExtractorPipelineSingleCas but it
>>> doesn't print anything related to relations.
>>>
>>> Could you please help me with extraction of relations from the med text ?
>>>
>>> As I am a new to ctakes and uima could you please provide step to step
>>> instructions and exact classes to use.
>>>
>>>
>>> Thanks in advance,
>>> Oleg.
>>>
>>> -----Original Message-----
>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>> Sent: 20 февраля 2017 г. 17:48
>>> To: dev@ctakes.apache.org
>>> Subject: Re: Ctakes relation extraction
>>>
>>> Hi Oleg,
>>>
>>> The relation extraction AE currently only handles location_of and
>>> degree_of relations as described here:
>>>
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/
>>>
>>> The dependencies are handled by the dependency parser (i.e. a separate
>>> module).
>>>
>>> So you’ll need to run both and collect all annotated relations from
>>> the the CAS.
>>>
>>> Hope this helps.
>>>
>>> Dima
>>>
>>>
>>>
>>>> On Feb 20, 2017, at 01:31, Oleg Bogatiryov <ol...@ctco.lv>
>>>> wrote:
>>>>
>>>> Hello to everyone.
>>>>
>>>>
>>>>
>>>> I am pleased to join the group.
>>>>
>>>>
>>>>
>>>> I am trying to extract relation from the document.
>>>>
>>>> Ideally I'd like to get the graph or tree of dependencies/relations
>>>> from the clinical documents.
>>>>
>>>>
>>>>
>>>> Could you please let me know how can I achieve it ?
>>>>
>>>>
>>>>
>>>> I am able to run CVD and RelationExtractorAggregate analysis engine
>>>> but there is no useful information
>>>>
>>>> in results that can be used in order to build a relation graph.
>>>>
>>>>
>>>>
>>>> Thanks in advance,
>>>>
>>>> Oleg.
>>>>
>>>
>>
>> <analysis_engine.zip.ze>
Re: [Relation_Extraction] Ctakes relation extraction
Posted by Oleg Bogatiryov <ol...@ctco.lv>.
Hi Dmitriy.
Thank you for your response.
Could you please let me know when the other types of relations will be released ?
Release number or date if possible please.
Thanks in advance.
----- Original Message -----
From: "ddligach" <dd...@luc.edu>
To: "Oleg Bogatiryov" <ol...@ctco.lv>
Cc: dev@ctakes.apache.org
Sent: Monday, March 6, 2017 8:08:01 PM
Subject: Re: [Relation_Extraction] Ctakes relation extraction
Hi Oleg,
Currently, cTAKES only includes the models for locationOf and DegreeOf relations. Even though I added the code for other relation types a while ago, we haven’t released the models (mostly because the performance on those relation types are not satisfactory).
So, you should just ignore everything except locationOf and degreeOf relations.
Hope this helps,
Dima
> On Mar 6, 2017, at 03:28, Oleg Bogatiryov <ol...@ctco.lv> wrote:
>
> Hi Dmitriy.
>
> Thank you for your response.
>
> I am using RelationExtractorPipeline class to generate xmi's.
> I got good results for LocationOfRelationExtractorAnnotator and
> DegreeOfRelationExtratorAnnotator.
>
> I've edited RelationExtractorAggregate.xml file with adding more annotators.
> There are some results but category is displayed like "O".
>
> For example working results:
>
> class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> Category: location_of
> Argument1: blood pressure
> Role: Argument
> Argument2: blood
> Role: Related_to
>
>
> class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
> Category: degree_of
> Argument1: anxiety
> Role: Argument
> Argument2: acute
> Role: Related_to
>
>
>
> And non-properly working
>
> class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
> Category: O
> Argument1: anxiety
> Role: Argument
> Argument2: anxiety
> Role: Related_to
>
> class
> org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
> Category: O
> Argument1: anxiety
> Role: Argument
> Argument2: symptoms
> Role: Related_to
>
> Category is O.
> Could you please help me with getting right results for other relations
> extraction annotators ?
>
> I've attached my ae descriptors. They are primitive and included into
> RelationExtractionAggregate.xml.
> Please remove .ze from the achive and uzip it.
>
> Thanks in advance,
> Oleg.
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Tuesday, February 28, 2017 1:58
> To: dev@ctakes.apache.org
> Subject: Re: Ctakes relation extraction
>
> Hi Oleg,
>
> You may want to look into learning about UIMA and UIMAFIT.
>
> Once you are somewhat comfortable with these frameworks, take a look at the
> package:
>
> ctakes/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/
>
> There are several pipelines that may work for you (e.g. take a look at
> RelationExtractorPipeline.java). Many of them should generate XMI files
> which contain the relation annotations you are looking for. Once you have
> generated the XMI files, you can parse them using UIMAFIT. E.g. take a look
> at RelationAnnotationViewer.java which you should use as an example.
>
> Hope this helps!
>
> Dima
>
>
>
>> On Feb 24, 2017, at 03:07, Oleg Bogatiryov <ol...@ctco.lv>
>> wrote:
>>
>> Hi Dmitriy.
>>
>> Thank you for your reply.
>>
>> I am not sure how can I extract location_of and degree_of.
>> AggregateTemplateFiller doesn't return anything in CVD as well as
>> TemporalAggregatePipeline.
>> There is BinaryTextRelation class that as I understand should fill in
>> relations but no data is displayed.
>>
>> I was trying to execute RelationExtractorPipelineSingleCas but it
>> doesn't print anything related to relations.
>>
>> Could you please help me with extraction of relations from the med text ?
>>
>> As I am a new to ctakes and uima could you please provide step to step
>> instructions and exact classes to use.
>>
>>
>> Thanks in advance,
>> Oleg.
>>
>> -----Original Message-----
>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> Sent: 20 февраля 2017 г. 17:48
>> To: dev@ctakes.apache.org
>> Subject: Re: Ctakes relation extraction
>>
>> Hi Oleg,
>>
>> The relation extraction AE currently only handles location_of and
>> degree_of relations as described here:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/
>>
>> The dependencies are handled by the dependency parser (i.e. a separate
>> module).
>>
>> So you’ll need to run both and collect all annotated relations from
>> the the CAS.
>>
>> Hope this helps.
>>
>> Dima
>>
>>
>>
>>> On Feb 20, 2017, at 01:31, Oleg Bogatiryov <ol...@ctco.lv>
>>> wrote:
>>>
>>> Hello to everyone.
>>>
>>>
>>>
>>> I am pleased to join the group.
>>>
>>>
>>>
>>> I am trying to extract relation from the document.
>>>
>>> Ideally I'd like to get the graph or tree of dependencies/relations
>>> from the clinical documents.
>>>
>>>
>>>
>>> Could you please let me know how can I achieve it ?
>>>
>>>
>>>
>>> I am able to run CVD and RelationExtractorAggregate analysis engine
>>> but there is no useful information
>>>
>>> in results that can be used in order to build a relation graph.
>>>
>>>
>>>
>>> Thanks in advance,
>>>
>>> Oleg.
>>>
>>
>
> <analysis_engine.zip.ze>