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Mon, 23 Sep 2013 15:43:44 PDT X-Rocket-MIMEInfo: 002.001,SGkgRGltYSwKCkkgcnVuIFJlbGF0aW9uRXh0cmFjdG9yUGlwZWxpbmVTaW5nbGVDYXMuamF2YSBhbmQgaSBnb3QgCmRlZ3JlZV9vZihzZXZlcmUgcGFpbi8zLCBzZXZlcmUvMikKZGVncmVlX29mKHBhaW4vMywgc2V2ZXJlLzIpCmxvY2F0aW9uX29mKHBhaW4vMywgd3Jpc3RzLzYpCgpidXQgd2hlbiBpIHJ1biBVSU1BX0NWRC0tcmVsYXRpb24tZXh0cmFjdG9yLmxhdW5jaCAtIG9yIFVJTUFfQ1BFLS1yZWxhdGlvbi1leHRyYWN0b3IubGF1bmNowqAgb24gdGhlIGh1cmQgY29kZWQgdGV4dMKgICJIZSBzdGlsbCABMAEBAQE- X-Mailer: YahooMailWebService/0.8.157.561 References: <996FC801C05DF64A84246A106FACACD01BA8CC@MSGPEXCHA08A.mfad.mfroot.org> <924DE05C19409B438EB81DE683A942D9105AFACA@CHEXMBX1A.CHBOSTON.ORG> <1379775648.14371.YahooMailNeo@web140304.mail.bf1.yahoo.com> <5240A6CB.1040301@childrens.harvard.edu> Message-ID: <1379976224.70868.YahooMailNeo@web140302.mail.bf1.yahoo.com> Date: Mon, 23 Sep 2013 15:43:44 -0700 (PDT) From: samir chabou Reply-To: samir chabou Subject: Re: examples of relation extractor annotations To: "dev@ctakes.apache.org" , "user@ctakes.apache.org" In-Reply-To: <5240A6CB.1040301@childrens.harvard.edu> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-686716756-1156944645-1379976224=:70868" X-Virus-Checked: Checked by ClamAV on apache.org ---686716756-1156944645-1379976224=:70868 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Dima,=0A=0AI run RelationExtractorPipelineSingleCas.java and i got =0Ade= gree_of(severe pain/3, severe/2)=0Adegree_of(pain/3, severe/2)=0Alocation_o= f(pain/3, wrists/6)=0A=0Abut when i run UIMA_CVD--relation-extractor.launch= - or UIMA_CPE--relation-extractor.launch=A0 on the hurd coded text=A0 "He = still is not able to work because of severe pain involving his wrists." the= re is no annotation of type: =0Aorg.apache.ctakes.typesystem.type.relation.= LocationOf=0Aorg.apache.ctakes.typesystem.type.relation.DegreeOf=0A=0A=0AI = need to identify the relations=A0 by their annotation type so i can iterate= on them=0A=0AThanks=0ASamir=0A=0A=0A=0A=0A________________________________= =0A From: Dmitriy Dligach =0ATo: dev= @ctakes.apache.org; samir chabou ; "user@ctakes.apache.= org" =0ASent: Monday, September 23, 2013 4:38:35 P= M=0ASubject: Re: examples of relation extractor annotations=0A =0A=0ASamir,= =0A=0ACould you please try to run ctakes-relation-extractor/src/main/java/o= rg/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingl= eCas.java and see if it finds any relations in the hard-coded sample senten= ce. In that sentence=0A=0A"He still is not able to work because of severe p= ain involving his wrists."=0A=0Ayou should see the following relations:=0A= =0Adegree_of(severe pain/3, severe/2)=0Adegree_of(pain/3, severe/2)=0Alocat= ion_of(pain/3, wrists/6)=0A=0Awhich will be printed to the console. The num= bers next to each argument are the UMLS semantic types (e.g. 6 =3D anatomic= al site).=0A=0ADima=0A=0AOn 09/21/2013 11:00 AM, samir chabou wrote:=0A> Hi= ,=0A> I tried to get examples of relation extractor annotations using Relat= ionExtractorAggregate.xml. I tried the RelationExtractorAggregate on many i= nput medical text but there was no annotation for any kind of relation. I e= ven tried the bellow text used in RelationExtractorAnnotatorsTest but again= no relation is annotated. Do you have idea or am i missing some thing ?=0A= >=A0 =A0 =A0 =A0 "He had a slight fracture in the proximal right fibula.",= =0A>=A0 =A0 =A0 =A0 =A0 "He had a slight fracture in the proximal right fib= ula .",=0A>=A0 =A0 =A0 =A0 =A0 "PRP VBD DT JJ NN IN DT JJ JJ NN .");=0A> = =0A> =0A> Thanks=0A> Samir=0A> =0A=0A-- Dmitriy Dligach, PhD=0AResearch Fel= low=0AChildren's Hospital Informatics Program=0ABoston Children's Hospital = and Harvard Medical School=0A(617) 919-3596 ---686716756-1156944645-1379976224=:70868 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Dima,

I run= RelationExtractorPipelineSingleCas.java and i got
degree_of(severe pai= n/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.Locatio= nOf
org.apache.ctakes.typesystem.type.relation.DegreeOf

I need to identify the relations  by their a= nnotation type so i can iterate on them

Thanks
Samir


= From: Dmitriy Dligach <= dmitriy.dligach@childrens.harvard.edu>
To: dev@ctakes.apache.org; samir chabou <samirchb@ya= hoo.com>; "user@ctakes.apache.org" <user@ctakes.apache.org>
<= b>Sent: Monday, September 23,= 2013 4:38:35 PM
Subject:<= /b> Re: examples of relation extractor annotations

Samir,

Could you please try to run cta= kes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pi= pelines/RelationExtractorPipelineSingleCas.java and see if it finds any rel= ations 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 se= e the following relations:

degree_of(severe pain/3, severe/2)
deg= ree_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 =3D anatomical site).

Dima

On 09/21/20= 13 11:00 AM, samir chabou wrote:
> Hi,
> I tried to get example= s 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 us= ed in RelationExtractorAnnotatorsTest but again no relation is annotated. D= o you have idea or am i missing some thing ?
>      &n= bsp; "He had a slight fracture in the proximal right fibula.",
> = ;         "He had a slight fracture in the proximal right fibula .",
>          "PRP V= BD DT JJ NN IN DT JJ JJ NN .");
>
>
> Thanks
> Sa= mir
>

-- Dmitriy Dligach, PhD
Research Fellow
Children'= s Hospital Informatics Program
Boston Children's Hospital and Harvard Me= dical School
(617) 919-3596



<= /body> ---686716756-1156944645-1379976224=:70868--