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Posted to dev@ctakes.apache.org by samir chabou <sa...@yahoo.com> on 2013/09/21 17:00:48 UTC
examples of relation extractor annotations
Hi,
I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
"He had a slight fracture in the proximal right fibula.",
"He had a slight fracture in the proximal right fibula .",
"PRP VBD DT JJ NN IN DT JJ JJ NN .");
Thanks
Samir
Re: examples of relation extractor annotations
Posted by samir chabou <sa...@yahoo.com>.
Thanks Dima for these extra info. that may help me
I'll try it and let you know.
Samir
________________________________
From: Dmitriy Dligach <dm...@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Tuesday, September 24, 2013 4:43:15 PM
Subject: Re: examples of relation extractor annotations
Samir,
Actually, the relations are represented in the type system differently.
Please take a look at the BinaryTextRelation type. If you'd like an
example of how to iterate over the relations, take a look at
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java.
Once you get a hold of each BinaryTextRelation, you can determine the
relation type by looking at the 'category' attribute.
Dima
On 09/23/2013 06:43 PM, samir chabou wrote:
> Hi Dima,
>
> I run RelationExtractorPipelineSingleCas.java and i got
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
> org.apache.ctakes.typesystem.type.relation.LocationOf
> org.apache.ctakes.typesystem.type.relation.DegreeOf
>
>
> I need to identify the relations by their annotation type so i can iterate on them
>
> Thanks
> Samir
>
>
>
>
> ________________________________
> From: Dmitriy Dligach <dm...@childrens.harvard.edu>
> To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Sent: Monday, September 23, 2013 4:38:35 PM
> Subject: Re: examples of relation extractor annotations
>
>
> Samir,
>
> Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
>
> "He still is not able to work because of severe pain involving his wrists."
>
> you should see the following relations:
>
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
>
> Dima
>
> On 09/21/2013 11:00 AM, samir chabou wrote:
>> Hi,
>> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
>> "He had a slight fracture in the proximal right fibula.",
>> "He had a slight fracture in the proximal right fibula .",
>> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>>
>>
>> Thanks
>> Samir
>>
> -- Dmitriy Dligach, PhD
> Research Fellow
> Children's Hospital Informatics Program
> Boston Children's Hospital and Harvard Medical School
> (617) 919-3596
--
Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by samir chabou <sa...@yahoo.com>.
Thanks Dima for these extra info. that may help me
I'll try it and let you know.
Samir
________________________________
From: Dmitriy Dligach <dm...@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Tuesday, September 24, 2013 4:43:15 PM
Subject: Re: examples of relation extractor annotations
Samir,
Actually, the relations are represented in the type system differently.
Please take a look at the BinaryTextRelation type. If you'd like an
example of how to iterate over the relations, take a look at
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java.
Once you get a hold of each BinaryTextRelation, you can determine the
relation type by looking at the 'category' attribute.
Dima
On 09/23/2013 06:43 PM, samir chabou wrote:
> Hi Dima,
>
> I run RelationExtractorPipelineSingleCas.java and i got
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
> org.apache.ctakes.typesystem.type.relation.LocationOf
> org.apache.ctakes.typesystem.type.relation.DegreeOf
>
>
> I need to identify the relations by their annotation type so i can iterate on them
>
> Thanks
> Samir
>
>
>
>
> ________________________________
> From: Dmitriy Dligach <dm...@childrens.harvard.edu>
> To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Sent: Monday, September 23, 2013 4:38:35 PM
> Subject: Re: examples of relation extractor annotations
>
>
> Samir,
>
> Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
>
> "He still is not able to work because of severe pain involving his wrists."
>
> you should see the following relations:
>
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
>
> Dima
>
> On 09/21/2013 11:00 AM, samir chabou wrote:
>> Hi,
>> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
>> "He had a slight fracture in the proximal right fibula.",
>> "He had a slight fracture in the proximal right fibula .",
>> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>>
>>
>> Thanks
>> Samir
>>
> -- Dmitriy Dligach, PhD
> Research Fellow
> Children's Hospital Informatics Program
> Boston Children's Hospital and Harvard Medical School
> (617) 919-3596
--
Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by samir chabou <sa...@yahoo.com>.
Hi Dima,
Just to let you know that I'm now able to iterate on the relations. I wrote the cas as xmi using the CPE and after i read it. The relations are in the xmi cas even though they don't appear on the CVD.
Thanks for your help
Samir
________________________________
From: Dmitriy Dligach <dm...@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Tuesday, September 24, 2013 4:43:15 PM
Subject: Re: examples of relation extractor annotations
Samir,
Actually, the relations are represented in the type system differently.
Please take a look at the BinaryTextRelation type. If you'd like an
example of how to iterate over the relations, take a look at
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java.
Once you get a hold of each BinaryTextRelation, you can determine the
relation type by looking at the 'category' attribute.
Dima
On 09/23/2013 06:43 PM, samir chabou wrote:
> Hi Dima,
>
> I run RelationExtractorPipelineSingleCas.java and i got
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
> org.apache.ctakes.typesystem.type.relation.LocationOf
> org.apache.ctakes.typesystem.type.relation.DegreeOf
>
>
> I need to identify the relations by their annotation type so i can iterate on them
>
> Thanks
> Samir
>
>
>
>
> ________________________________
> From: Dmitriy Dligach <dm...@childrens.harvard.edu>
> To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Sent: Monday, September 23, 2013 4:38:35 PM
> Subject: Re: examples of relation extractor annotations
>
>
> Samir,
>
> Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
>
> "He still is not able to work because of severe pain involving his wrists."
>
> you should see the following relations:
>
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
>
> Dima
>
> On 09/21/2013 11:00 AM, samir chabou wrote:
>> Hi,
>> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
>> "He had a slight fracture in the proximal right fibula.",
>> "He had a slight fracture in the proximal right fibula .",
>> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>>
>>
>> Thanks
>> Samir
>>
> -- Dmitriy Dligach, PhD
> Research Fellow
> Children's Hospital Informatics Program
> Boston Children's Hospital and Harvard Medical School
> (617) 919-3596
--
Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by Dmitriy Dligach <dm...@childrens.harvard.edu>.
Samir,
Actually, the relations are represented in the type system differently.
Please take a look at the BinaryTextRelation type. If you'd like an
example of how to iterate over the relations, take a look at
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java.
Once you get a hold of each BinaryTextRelation, you can determine the
relation type by looking at the 'category' attribute.
Dima
On 09/23/2013 06:43 PM, samir chabou wrote:
> Hi Dima,
>
> I run RelationExtractorPipelineSingleCas.java and i got
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
> org.apache.ctakes.typesystem.type.relation.LocationOf
> org.apache.ctakes.typesystem.type.relation.DegreeOf
>
>
> I need to identify the relations by their annotation type so i can iterate on them
>
> Thanks
> Samir
>
>
>
>
> ________________________________
> From: Dmitriy Dligach <dm...@childrens.harvard.edu>
> To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
> Sent: Monday, September 23, 2013 4:38:35 PM
> Subject: Re: examples of relation extractor annotations
>
>
> Samir,
>
> Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
>
> "He still is not able to work because of severe pain involving his wrists."
>
> you should see the following relations:
>
> degree_of(severe pain/3, severe/2)
> degree_of(pain/3, severe/2)
> location_of(pain/3, wrists/6)
>
> which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
>
> Dima
>
> On 09/21/2013 11:00 AM, samir chabou wrote:
>> Hi,
>> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
>> "He had a slight fracture in the proximal right fibula.",
>> "He had a slight fracture in the proximal right fibula .",
>> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>>
>>
>> Thanks
>> Samir
>>
> -- Dmitriy Dligach, PhD
> Research Fellow
> Children's Hospital Informatics Program
> Boston Children's Hospital and Harvard Medical School
> (617) 919-3596
--
Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by samir chabou <sa...@yahoo.com>.
Hi Dima,
I run RelationExtractorPipelineSingleCas.java and i got
degree_of(severe pain/3, severe/2)
degree_of(pain/3, severe/2)
location_of(pain/3, wrists/6)
but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
org.apache.ctakes.typesystem.type.relation.LocationOf
org.apache.ctakes.typesystem.type.relation.DegreeOf
I need to identify the relations by their annotation type so i can iterate on them
Thanks
Samir
________________________________
From: Dmitriy Dligach <dm...@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Monday, September 23, 2013 4:38:35 PM
Subject: Re: examples of relation extractor annotations
Samir,
Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
"He still is not able to work because of severe pain involving his wrists."
you should see the following relations:
degree_of(severe pain/3, severe/2)
degree_of(pain/3, severe/2)
location_of(pain/3, wrists/6)
which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
Dima
On 09/21/2013 11:00 AM, samir chabou wrote:
> Hi,
> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
> "He had a slight fracture in the proximal right fibula.",
> "He had a slight fracture in the proximal right fibula .",
> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>
>
> Thanks
> Samir
>
-- Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by samir chabou <sa...@yahoo.com>.
Hi Dima,
I run RelationExtractorPipelineSingleCas.java and i got
degree_of(severe pain/3, severe/2)
degree_of(pain/3, severe/2)
location_of(pain/3, wrists/6)
but when i run UIMA_CVD--relation-extractor.launch - or UIMA_CPE--relation-extractor.launch on the hurd coded text "He still is not able to work because of severe pain involving his wrists." there is no annotation of type:
org.apache.ctakes.typesystem.type.relation.LocationOf
org.apache.ctakes.typesystem.type.relation.DegreeOf
I need to identify the relations by their annotation type so i can iterate on them
Thanks
Samir
________________________________
From: Dmitriy Dligach <dm...@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <sa...@yahoo.com>; "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Monday, September 23, 2013 4:38:35 PM
Subject: Re: examples of relation extractor annotations
Samir,
Could you please try to run ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java and see if it finds any relations in the hard-coded sample sentence. In that sentence
"He still is not able to work because of severe pain involving his wrists."
you should see the following relations:
degree_of(severe pain/3, severe/2)
degree_of(pain/3, severe/2)
location_of(pain/3, wrists/6)
which will be printed to the console. The numbers next to each argument are the UMLS semantic types (e.g. 6 = anatomical site).
Dima
On 09/21/2013 11:00 AM, samir chabou wrote:
> Hi,
> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
> "He had a slight fracture in the proximal right fibula.",
> "He had a slight fracture in the proximal right fibula .",
> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>
>
> Thanks
> Samir
>
-- Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596
Re: examples of relation extractor annotations
Posted by Dmitriy Dligach <dm...@childrens.harvard.edu>.
Samir,
Could you please try to run
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java
and see if it finds any relations in the hard-coded sample sentence. In
that sentence
"He still is not able to work because of severe pain involving his wrists."
you should see the following relations:
degree_of(severe pain/3, severe/2)
degree_of(pain/3, severe/2)
location_of(pain/3, wrists/6)
which will be printed to the console. The numbers next to each argument
are the UMLS semantic types (e.g. 6 = anatomical site).
Dima
On 09/21/2013 11:00 AM, samir chabou wrote:
> Hi,
> I tried to get examples of relation extractor annotations using RelationExtractorAggregate.xml. I tried the RelationExtractorAggregate on many input medical text but there was no annotation for any kind of relation. I even tried the bellow text used in RelationExtractorAnnotatorsTest but again no relation is annotated. Do you have idea or am i missing some thing ?
> "He had a slight fracture in the proximal right fibula.",
> "He had a slight fracture in the proximal right fibula .",
> "PRP VBD DT JJ NN IN DT JJ JJ NN .");
>
>
> Thanks
> Samir
>
--
Dmitriy Dligach, PhD
Research Fellow
Children's Hospital Informatics Program
Boston Children's Hospital and Harvard Medical School
(617) 919-3596